Variant report

Variant	rs4544576
Chromosome Location	chr3:139143196-139143197
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139141697..139144068-chr3:139149999..139151730,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1044826	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10460845	0.95[ASN][1000 genomes]
rs10935320	0.90[ASN][1000 genomes]
rs10935323	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12488939	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12494556	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494806	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695698	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695699	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695700	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060697	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13071857	0.82[EUR][1000 genomes]
rs13074208	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13083195	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13085888	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086868	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089007	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13089052	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089090	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13092507	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092935	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586861	0.90[ASN][1000 genomes]
rs1586863	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1586864	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17336869	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1907687	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165139	0.84[ASN][1000 genomes]
rs2233811	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233815	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2349059	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34623690	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772877	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772878	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772879	0.88[ASN][1000 genomes]
rs3821544	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821545	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683818	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67929453	0.92[ASN][1000 genomes]
rs7374385	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs747346	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289576	0.95[CEU][hapmap]
rs9289578	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs964227	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs973691	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9812192	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9818691	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825064	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9831108	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834607	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9835241	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848241	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849039	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849578	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9853350	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860201	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860521	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9868544	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882014	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139114200-139153800	Weak transcription	Left Ventricle	heart
2	chr3:139133200-139144200	Weak transcription	Right Ventricle	heart
3	chr3:139133800-139144200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
5	chr3:139137200-139149200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:139137400-139146400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:139137600-139144600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:139137600-139146400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:139137800-139153200	Weak transcription	Esophagus	oesophagus
10	chr3:139138000-139144600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:139138200-139153600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:139138400-139146600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:139138600-139147800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:139139600-139144600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:139139600-139160000	Weak transcription	Fetal Brain Male	brain
18	chr3:139140400-139143800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:139140400-139146400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:139140400-139146600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:139140400-139146600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:139140600-139145200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:139140600-139146600	Weak transcription	Fetal Kidney	kidney
24	chr3:139140600-139147200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:139140800-139143400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:139140800-139147200	Weak transcription	Brain Germinal Matrix	brain
27	chr3:139140800-139152800	Weak transcription	Placenta	Placenta
28	chr3:139140800-139153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:139140800-139153200	Weak transcription	HSMMtube	muscle
30	chr3:139140800-139153800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:139141000-139143600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:139141200-139160000	Weak transcription	Lung	lung
33	chr3:139141400-139146800	Weak transcription	Fetal Intestine Large	intestine
34	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:139141800-139144400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:139142000-139144800	Strong transcription	Adipose Nuclei	Adipose
37	chr3:139142000-139145000	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:139142000-139145200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:139142000-139146600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:139142000-139146600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:139142000-139147400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:139142200-139143400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr3:139142200-139143400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:139142200-139143400	Weak transcription	Pancreas	Pancrea
45	chr3:139142200-139143600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:139142200-139143600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:139142200-139143600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:139142200-139144800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:139142200-139145200	Strong transcription	Brain Hippocampus Middle	brain
50	chr3:139142200-139146600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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