Variant report

Variant	rs2339968
Chromosome Location	chr3:179899137-179899138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10222466	0.91[EUR][1000 genomes]
rs10513771	0.86[ASN][1000 genomes]
rs10937020	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10937021	0.88[EUR][1000 genomes]
rs11709960	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718127	0.81[ASN][1000 genomes]
rs12487650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492526	0.95[ASN][1000 genomes]
rs12636328	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13322790	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357904	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1404743	0.84[ASN][1000 genomes]
rs1404744	0.90[EUR][1000 genomes]
rs1464844	0.86[EUR][1000 genomes]
rs1464845	0.85[ASN][1000 genomes]
rs1525269	0.87[EUR][1000 genomes]
rs1525272	0.85[EUR][1000 genomes]
rs1525276	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1525277	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1568859	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568860	0.96[ASN][1000 genomes]
rs1581549	0.86[EUR][1000 genomes]
rs1589858	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831126	0.81[ASN][1000 genomes]
rs16831219	0.90[ASN][1000 genomes]
rs16831288	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1852121	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1852122	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1852123	0.84[EUR][1000 genomes]
rs1921676	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1950124	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049472	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2091273	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2177723	0.91[ASN][1000 genomes]
rs2339967	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879654	0.96[ASN][1000 genomes]
rs28865282	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849420	0.96[EUR][1000 genomes]
rs3906013	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3906014	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4109306	0.85[EUR][1000 genomes]
rs4854901	0.81[ASN][1000 genomes]
rs4854902	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854903	0.86[ASN][1000 genomes]
rs4854961	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854962	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4854964	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4854966	0.85[ASN][1000 genomes]
rs56234136	0.85[ASN][1000 genomes]
rs59555202	0.84[EUR][1000 genomes]
rs60057308	0.81[ASN][1000 genomes]
rs62290558	0.81[ASN][1000 genomes]
rs62292283	0.87[ASN][1000 genomes]
rs62292284	0.87[ASN][1000 genomes]
rs62292290	0.85[ASN][1000 genomes]
rs62292291	0.85[ASN][1000 genomes]
rs62292292	0.83[ASN][1000 genomes]
rs6790229	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790465	0.91[EUR][1000 genomes]
rs67979781	0.81[ASN][1000 genomes]
rs68014168	0.88[ASN][1000 genomes]
rs6803764	0.81[EUR][1000 genomes]
rs7619775	0.87[EUR][1000 genomes]
rs7621628	0.94[EUR][1000 genomes]
rs7622125	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7635210	0.83[EUR][1000 genomes]
rs7652322	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7652473	0.81[ASN][1000 genomes]
rs9290696	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290697	0.90[EUR][1000 genomes]
rs9812621	0.87[EUR][1000 genomes]
rs9819178	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821124	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9837718	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840477	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840775	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845934	0.88[EUR][1000 genomes]
rs9851723	0.84[EUR][1000 genomes]
rs9857420	0.87[EUR][1000 genomes]
rs9860526	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862989	0.90[EUR][1000 genomes]
rs9863693	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9868908	0.85[EUR][1000 genomes]
rs9869517	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871928	0.81[ASN][1000 genomes]
rs9871936	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877454	0.86[EUR][1000 genomes]
rs9880357	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179897000-179899200	Enhancers	Adipose Nuclei	Adipose
2	chr3:179897800-179899800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:179897800-179900000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:179898000-179899200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:179898200-179899200	Enhancers	Osteobl	bone
6	chr3:179898200-179899800	Enhancers	HMEC	breast
7	chr3:179899000-179899200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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