Variant report

Variant	rs58774466
Chromosome Location	chr3:180333876-180333877
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:180319483..180321935-chr3:180330733..180334289,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163728	Chromatin interaction
ENSG00000239774	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16831798	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338435	0.85[AMR][1000 genomes]
rs34373335	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4854982	0.85[AMR][1000 genomes]
rs55969409	0.85[AMR][1000 genomes]
rs62292365	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62292366	0.85[AMR][1000 genomes]
rs62292369	0.85[AMR][1000 genomes]
rs62292371	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7612917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3359190	chr3:180298396-180397223	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180320600-180337400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:180320600-180343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:180320600-180343800	Weak transcription	Spleen	Spleen
4	chr3:180320600-180344200	Weak transcription	Esophagus	oesophagus
5	chr3:180320600-180344200	Weak transcription	Gastric	stomach
6	chr3:180320800-180344000	Weak transcription	Pancreas	Pancrea
7	chr3:180320800-180344400	Weak transcription	Aorta	Aorta
8	chr3:180321000-180334200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:180321600-180342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:180321800-180342400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:180322200-180336200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:180323400-180343600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:180323400-180343600	Weak transcription	Fetal Stomach	stomach
14	chr3:180327800-180335600	Weak transcription	Small Intestine	intestine
15	chr3:180328200-180337800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:180329400-180336400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:180329400-180349400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:180329600-180339200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:180329600-180340000	Weak transcription	Fetal Brain Male	brain
20	chr3:180329600-180348600	Weak transcription	Psoas Muscle	Psoas
21	chr3:180329800-180334600	Weak transcription	K562	blood
22	chr3:180329800-180335000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:180330600-180343600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:180330600-180343800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:180330600-180344000	Weak transcription	Lung	lung
26	chr3:180330600-180345400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:180330600-180346000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:180330600-180346000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:180330600-180346000	Weak transcription	Ovary	ovary
30	chr3:180330600-180346200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:180330600-180347400	Weak transcription	Left Ventricle	heart
32	chr3:180330800-180336800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:180330800-180344200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:180330800-180345600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:180330800-180346200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:180330800-180346400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:180331000-180335200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:180331000-180335600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:180331000-180343000	Weak transcription	Osteobl	bone
40	chr3:180331000-180343400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:180331200-180343400	Weak transcription	NHLF	lung
42	chr3:180331200-180344200	Weak transcription	Brain Germinal Matrix	brain
43	chr3:180331200-180346200	Weak transcription	Thymus	Thymus
44	chr3:180331200-180346200	Weak transcription	A549	lung
45	chr3:180331200-180346800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:180331200-180347800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:180331200-180348000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:180331200-180348000	Weak transcription	NHEK	skin
49	chr3:180331400-180335200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:180331400-180337200	Weak transcription	Duodenum Mucosa	Duodenum

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