Variant report

Variant	rs16853999
Chromosome Location	chr3:143378381-143378382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10513216	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10935500	0.92[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1242054	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs1242057	1.00[ASN][1000 genomes]
rs12629688	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs13059265	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1345170	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs1447741	0.83[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1534162	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs16854008	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs1868174	0.83[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1868175	0.81[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1868177	0.85[ASN][1000 genomes]
rs2121777	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs4566534	0.91[GIH][hapmap];0.83[LWK][hapmap];0.88[AFR][1000 genomes]
rs4839649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4839650	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs4839651	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs57630925	1.00[ASN][1000 genomes]
rs57917966	1.00[ASN][1000 genomes]
rs58441250	1.00[ASN][1000 genomes]
rs58652978	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60098452	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60428559	0.98[ASN][1000 genomes]
rs60633318	1.00[ASN][1000 genomes]
rs60891486	0.85[ASN][1000 genomes]
rs61645302	1.00[ASN][1000 genomes]
rs62269851	0.98[ASN][1000 genomes]
rs62269855	1.00[ASN][1000 genomes]
rs62269856	1.00[ASN][1000 genomes]
rs62270560	1.00[ASN][1000 genomes]
rs6440181	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs6774032	0.83[JPT][hapmap]
rs6774050	0.81[CHB][hapmap]
rs6782154	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs6803893	0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs7629784	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7629855	1.00[ASN][1000 genomes]
rs7650371	0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7650396	0.87[ASN][1000 genomes]
rs935519	0.83[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs935520	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9831286	0.86[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs9844600	0.87[ASN][1000 genomes]
rs9882472	0.92[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143363600-143379000	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:143367400-143390400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:143370400-143390400	Weak transcription	Fetal Lung	lung
4	chr3:143370800-143420800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143371200-143383000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:143374200-143382800	Weak transcription	Esophagus	oesophagus
7	chr3:143374600-143378600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:143376200-143378600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:143377200-143378400	Enhancers	Pancreatic Islets	Pancreatic Islet

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