Variant report

Variant	rs3857059
Chromosome Location	chr4:90675238-90675239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10003708	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10025915	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10033209	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433953	0.82[ASN][1000 genomes]
rs1045722	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516844	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516845	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11931062	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11931074	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11935469	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11944331	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11945223	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640100	0.97[ASN][1000 genomes]
rs12642514	0.94[ASN][1000 genomes]
rs12648141	1.00[ASN][1000 genomes]
rs17016071	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016193	0.89[CEU][hapmap]
rs17016235	0.89[CEU][hapmap]
rs2736990	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2737029	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs28393675	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28412513	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613708	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28781297	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35495602	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35541731	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs356165	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs356168	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs356200	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap]
rs356203	1.00[ASN][1000 genomes]
rs356204	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs356219	0.96[ASN][1000 genomes]
rs3756054	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775422	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775423	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775424	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3775427	0.83[ASN][1000 genomes]
rs3775433	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775434	0.83[ASN][1000 genomes]
rs3775439	0.86[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs3796661	0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3822086	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822089	0.83[ASN][1000 genomes]
rs3822090	0.89[CEU][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3857051	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857052	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857053	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857058	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857061	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3899608	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3933594	0.88[AMR][1000 genomes]
rs4031753	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4088093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4088094	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4122861	0.87[ASN][1000 genomes]
rs58054215	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60031383	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61032876	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532190	0.89[CEU][hapmap]
rs6818319	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6826785	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6834765	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73831461	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7436973	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7655611	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7655792	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7661330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675290	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681312	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681815	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7684318	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690873	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7698672	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8180209	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180214	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894278	0.89[CEU][hapmap]

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	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

No data

Chromatin state (count:40 , 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	chr4:90664600-90678000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:90673400-90679200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:90674000-90675400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:90674000-90675400	Enhancers	Fetal Intestine Small	intestine
7	chr4:90674000-90675400	Enhancers	Fetal Lung	lung
8	chr4:90674000-90675400	Enhancers	Placenta	Placenta
9	chr4:90674000-90676000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:90674000-90676000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:90674200-90675400	Strong transcription	Primary hematopoietic stem cells	blood
12	chr4:90674200-90675400	Enhancers	Brain Anterior Caudate	brain
13	chr4:90674200-90675400	Enhancers	Fetal Intestine Large	intestine
14	chr4:90674400-90675800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:90674600-90675400	Enhancers	A549	lung
16	chr4:90674600-90682000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:90674800-90675400	Enhancers	Hela-S3	cervix
18	chr4:90674800-90675400	Enhancers	Osteobl	bone
19	chr4:90674800-90675600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:90674800-90677000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:90675000-90675400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:90675000-90675400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:90675000-90675400	Enhancers	NH-A	brain
24	chr4:90675000-90676000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:90675000-90676000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:90675000-90676000	Enhancers	HMEC	breast
27	chr4:90675000-90676000	Enhancers	NHDF-Ad	bronchial
28	chr4:90675000-90676000	Enhancers	NHEK	skin
29	chr4:90675000-90676200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr4:90675000-90676200	Enhancers	HUVEC	blood vessel
31	chr4:90675000-90678400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:90675000-90680000	Weak transcription	NHLF	lung
33	chr4:90675000-90680200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:90675000-90683800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:90675000-90686200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:90675000-90687000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:90675200-90675400	Active TSS	Fetal Brain Male	brain
38	chr4:90675200-90680000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:90675200-90686000	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:90675200-90687000	Weak transcription	Fetal Kidney	kidney

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