Variant report

Variant	rs3756054
Chromosome Location	chr4:90674451-90674452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90673252..90674958-chr4:90721140..90722771,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10003708	0.95[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];0.96[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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516844	0.91[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	0.93[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	0.90[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	0.98[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]
rs3775422	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775423	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap];0.96[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	0.95[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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857052	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3857053	0.97[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]
rs3857059	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]
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	0.95[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	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6532190	0.89[CEU][hapmap]
rs6818319	0.93[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	0.96[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	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7661330	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675290	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681312	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7681815	0.91[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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180214	0.98[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:72 , 50 per page) page: 1 2

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	chr4:90673400-90674600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:90673400-90679200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:90673800-90675000	Enhancers	Rectal Smooth Muscle	rectum
7	chr4:90674000-90674600	Enhancers	Fetal Brain Male	brain
8	chr4:90674000-90674800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:90674000-90674800	Enhancers	Brain Substantia Nigra	brain
10	chr4:90674000-90674800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr4:90674000-90674800	Enhancers	Ovary	ovary
12	chr4:90674000-90674800	Flanking Active TSS	Hela-S3	cervix
13	chr4:90674000-90674800	Enhancers	HSMMtube	muscle
14	chr4:90674000-90675000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:90674000-90675000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:90674000-90675000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:90674000-90675000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:90674000-90675000	Enhancers	Brain Angular Gyrus	brain
19	chr4:90674000-90675000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr4:90674000-90675000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:90674000-90675000	Enhancers	Fetal Heart	heart
22	chr4:90674000-90675000	Enhancers	Fetal Stomach	stomach
23	chr4:90674000-90675000	Flanking Active TSS	HUVEC	blood vessel
24	chr4:90674000-90675200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:90674000-90675200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr4:90674000-90675200	Enhancers	Brain Cingulate Gyrus	brain
27	chr4:90674000-90675200	Enhancers	Brain Hippocampus Middle	brain
28	chr4:90674000-90675200	Enhancers	Fetal Kidney	kidney
29	chr4:90674000-90675200	Enhancers	Stomach Smooth Muscle	stomach
30	chr4:90674000-90675400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:90674000-90675400	Enhancers	Fetal Intestine Small	intestine
32	chr4:90674000-90675400	Enhancers	Fetal Lung	lung
33	chr4:90674000-90675400	Enhancers	Placenta	Placenta
34	chr4:90674000-90676000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:90674000-90676000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:90674200-90674600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:90674200-90674600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:90674200-90674600	Enhancers	Small Intestine	intestine
39	chr4:90674200-90674800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr4:90674200-90674800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr4:90674200-90674800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:90674200-90674800	Enhancers	Fetal Muscle Leg	muscle
43	chr4:90674200-90674800	Enhancers	Left Ventricle	heart
44	chr4:90674200-90674800	Enhancers	Right Atrium	heart
45	chr4:90674200-90674800	Flanking Active TSS	Osteobl	bone
46	chr4:90674200-90675000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr4:90674200-90675000	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:90674200-90675000	Enhancers	HSMM	muscle
49	chr4:90674200-90675000	Flanking Active TSS	NH-A	brain
50	chr4:90674200-90675000	Flanking Active TSS	NHDF-Ad	bronchial

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