Variant report

Variant	rs12054089
Chromosome Location	chr3:81691855-81691856
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12629752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638507	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088641	0.84[MEX][hapmap]
rs13097903	0.91[MEX][hapmap]
rs17019219	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17019297	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2680270	0.86[AFR][1000 genomes]
rs3772888	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3772897	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772899	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs3772902	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs3772904	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60509885	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs998206	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933756	chr3:81413060-81754738	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1003217	chr3:81435044-81752521	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv933259	chr3:81523854-81730617	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv999587	chr3:81534364-81707800	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv536603	chr3:81534364-81707800	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81603600-81726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:81613600-81699200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:81614000-81693600	Weak transcription	Aorta	Aorta
4	chr3:81627400-81755000	Weak transcription	Primary B cells from cord blood	blood
5	chr3:81635000-81700800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:81642000-81753000	Weak transcription	HUVEC	blood vessel
7	chr3:81642200-81712200	Weak transcription	Ovary	ovary
8	chr3:81662200-81699800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:81662200-81703000	Weak transcription	HSMMtube	muscle
10	chr3:81675600-81699600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:81675800-81696400	Weak transcription	HMEC	breast
12	chr3:81676000-81692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:81678400-81696800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:81678600-81701600	Strong transcription	Dnd41	blood
15	chr3:81680000-81692600	Weak transcription	GM12878-XiMat	blood
16	chr3:81680600-81698200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:81680600-81703000	Weak transcription	Hela-S3	cervix
18	chr3:81681200-81699600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:81682400-81706600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:81682600-81692000	Weak transcription	NHDF-Ad	bronchial
21	chr3:81683400-81699000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:81684400-81712400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:81686600-81699000	Weak transcription	NHLF	lung
24	chr3:81687400-81700600	Weak transcription	NH-A	brain
25	chr3:81687600-81696800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:81688000-81692600	Weak transcription	Primary T cells from cord blood	blood
27	chr3:81688000-81699200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:81688200-81693200	Weak transcription	Fetal Heart	heart
29	chr3:81688800-81695400	Strong transcription	Adipose Nuclei	Adipose
30	chr3:81688800-81696200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:81689000-81712200	Weak transcription	Lung	lung
32	chr3:81689600-81692000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:81689600-81694600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:81689600-81699000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:81689600-81699800	Weak transcription	Psoas Muscle	Psoas
36	chr3:81689600-81712200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:81689600-81726200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:81689600-81744000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:81689800-81694200	Weak transcription	Left Ventricle	heart
40	chr3:81689800-81744000	Weak transcription	Right Ventricle	heart
41	chr3:81690600-81692200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:81690600-81693000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:81691200-81692800	Strong transcription	Osteobl	bone
44	chr3:81691200-81693200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:81691400-81694400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:81691400-81695000	Weak transcription	HSMM	muscle
47	chr3:81691800-81694000	Strong transcription	HepG2	liver
48	chr3:81691800-81695200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:81691800-81696600	Strong transcription	Liver	Liver

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