Variant report

Variant	rs3796661
Chromosome Location	chr4:90687507-90687508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10003708	0.81[ASN][1000 genomes]
rs10025915	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10033209	0.83[ASN][1000 genomes]
rs10433953	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1045722	0.83[ASN][1000 genomes]
rs10516844	0.80[ASN][1000 genomes]
rs10516845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11931062	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11931074	0.80[ASN][1000 genomes]
rs11935469	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11944331	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11945223	0.81[ASN][1000 genomes]
rs12640100	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12642514	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12648141	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17016071	0.83[ASN][1000 genomes]
rs17016168	1.00[ASW][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs17016255	0.83[YRI][hapmap]
rs2035268	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs2737029	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs28393675	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28412513	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28613708	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28781297	1.00[ASN][1000 genomes]
rs35495602	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35541731	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs356165	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs356203	0.83[ASN][1000 genomes]
rs3756054	0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3756056	0.83[YRI][hapmap]
rs3775422	0.81[ASN][1000 genomes]
rs3775423	0.83[ASN][1000 genomes]
rs3775424	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775427	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775433	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3775434	1.00[ASN][1000 genomes]
rs3775439	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs3822086	0.83[ASN][1000 genomes]
rs3822089	1.00[ASN][1000 genomes]
rs3822090	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3857049	0.89[EUR][1000 genomes]
rs3857051	0.81[ASN][1000 genomes]
rs3857052	0.82[ASN][1000 genomes]
rs3857053	0.83[ASN][1000 genomes]
rs3857057	0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3857058	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3857059	0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3857061	1.00[ASN][1000 genomes]
rs3899608	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3906824	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs3910104	0.80[JPT][hapmap]
rs4031753	1.00[ASN][1000 genomes]
rs4088093	0.83[ASN][1000 genomes]
rs4088094	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4122861	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58054215	1.00[ASN][1000 genomes]
rs60031383	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61032876	0.81[ASN][1000 genomes]
rs6818319	0.80[ASN][1000 genomes]
rs6822088	0.92[ASN][1000 genomes]
rs6826785	0.99[ASN][1000 genomes]
rs6834765	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7436973	0.82[ASN][1000 genomes]
rs7655611	1.00[ASN][1000 genomes]
rs7655792	0.81[ASN][1000 genomes]
rs7661330	0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7675290	0.83[ASN][1000 genomes]
rs7681312	0.80[ASN][1000 genomes]
rs7681815	0.80[ASN][1000 genomes]
rs7684318	0.83[ASN][1000 genomes]
rs7690873	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7698672	1.00[ASN][1000 genomes]
rs8180209	0.83[ASN][1000 genomes]
rs8180214	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90649400-90696400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90663400-90691400	Weak transcription	Dnd41	blood
3	chr4:90675400-90696200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:90676200-90709200	Weak transcription	HUVEC	blood vessel
5	chr4:90683600-90689200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:90685200-90696400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:90686000-90687800	Enhancers	Brain Hippocampus Middle	brain
8	chr4:90686200-90687600	Enhancers	Brain Anterior Caudate	brain
9	chr4:90686200-90687600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr4:90686200-90688200	Enhancers	Brain Substantia Nigra	brain
11	chr4:90686400-90687600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:90686400-90687600	Enhancers	NHEK	skin
13	chr4:90686800-90687600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:90686800-90687600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:90686800-90687600	Enhancers	Fetal Stomach	stomach
16	chr4:90686800-90687800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:90686800-90687800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:90686800-90687800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:90686800-90687800	Enhancers	Fetal Heart	heart
20	chr4:90686800-90688000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr4:90687000-90687600	Enhancers	Adipose Nuclei	Adipose
22	chr4:90687000-90688000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:90687200-90687600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:90687200-90687600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:90687200-90691200	Weak transcription	Brain Angular Gyrus	brain
26	chr4:90687200-90718400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:90687400-90687600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:90687400-90688200	Enhancers	Fetal Lung	lung
29	chr4:90687400-90691000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:90687400-90697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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