Variant report

Variant	rs6780998
Chromosome Location	chr3:179996119-179996120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10222466	0.83[ASN][1000 genomes]
rs10755138	0.90[EUR][1000 genomes]
rs10937022	0.83[ASN][1000 genomes]
rs12108143	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12108145	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12633042	0.83[ASN][1000 genomes]
rs12638766	0.88[ASN][1000 genomes]
rs1464844	0.87[ASN][1000 genomes]
rs1520613	0.84[EUR][1000 genomes]
rs1525269	0.87[ASN][1000 genomes]
rs1525272	0.90[ASN][1000 genomes]
rs1581549	0.86[ASN][1000 genomes]
rs1589858	0.84[AFR][1000 genomes]
rs1608796	0.85[ASN][1000 genomes]
rs16831259	0.83[ASN][1000 genomes]
rs1852123	0.91[ASN][1000 genomes]
rs2030763	0.86[ASN][1000 genomes]
rs2178582	0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2222858	0.84[ASN][1000 genomes]
rs2337368	0.96[EUR][1000 genomes]
rs2337369	0.88[EUR][1000 genomes]
rs3849424	0.88[EUR][1000 genomes]
rs3849425	0.88[EUR][1000 genomes]
rs3849426	0.88[EUR][1000 genomes]
rs3906012	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3914869	0.88[EUR][1000 genomes]
rs3914871	0.88[EUR][1000 genomes]
rs4108253	0.94[EUR][1000 genomes]
rs4109306	0.92[ASN][1000 genomes]
rs4241377	0.96[EUR][1000 genomes]
rs4343625	0.83[ASN][1000 genomes]
rs4568133	0.88[EUR][1000 genomes]
rs4854907	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4854968	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4854969	0.88[EUR][1000 genomes]
rs55996463	0.84[EUR][1000 genomes]
rs57131411	0.91[ASN][1000 genomes]
rs62292286	0.83[ASN][1000 genomes]
rs62292288	0.83[ASN][1000 genomes]
rs62292294	0.85[ASN][1000 genomes]
rs6769259	0.84[EUR][1000 genomes]
rs6790465	0.84[ASN][1000 genomes]
rs7619775	0.87[ASN][1000 genomes]
rs7621628	0.80[ASN][1000 genomes]
rs7622865	0.97[EUR][1000 genomes]
rs7639931	0.99[EUR][1000 genomes]
rs7643438	0.94[EUR][1000 genomes]
rs7652473	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9290697	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs939441	0.91[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs9682110	0.88[EUR][1000 genomes]
rs9812621	0.86[ASN][1000 genomes]
rs9815922	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9815923	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9818172	0.88[EUR][1000 genomes]
rs9824544	0.88[EUR][1000 genomes]
rs9845934	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9860910	0.88[EUR][1000 genomes]
rs9862989	0.85[ASN][1000 genomes]
rs9864534	0.85[EUR][1000 genomes]
rs9867767	0.81[EUR][1000 genomes]
rs9868908	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9869873	0.98[EUR][1000 genomes]
rs9877454	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6780998	SENP2	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179993000-179998600	Weak transcription	NHDF-Ad	bronchial
2	chr3:179993000-180002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:179993600-179996200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:179993600-179998400	Weak transcription	HMEC	breast
5	chr3:179994200-179998600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:179994200-179999000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:179994800-179996800	Enhancers	Brain Substantia Nigra	brain
8	chr3:179995600-179997000	Enhancers	Primary B cells from peripheral blood	blood
9	chr3:179995600-179997800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:179995800-179997400	Flanking Active TSS	GM12878-XiMat	blood

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