Variant report

Variant	rs6789541
Chromosome Location	chr3:136330721-136330722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13433980	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1484250	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16843991	0.81[AMR][1000 genomes]
rs28682370	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34962604	0.82[EUR][1000 genomes]
rs35644083	0.81[EUR][1000 genomes]
rs3932048	0.82[AMR][1000 genomes]
rs4336059	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4402873	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55993001	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56040643	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56047785	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59931907	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6439642	0.81[AMR][1000 genomes]
rs66810260	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6763239	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6765239	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769934	0.84[EUR][1000 genomes]
rs6772759	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6782151	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6788346	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6789761	0.81[EUR][1000 genomes]
rs6800969	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6806795	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7612160	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7621017	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7621970	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7623824	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626418	0.82[EUR][1000 genomes]
rs7627292	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7629905	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7644346	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7644471	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812319	0.83[EUR][1000 genomes]
rs9818372	0.84[EUR][1000 genomes]
rs9820513	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9828068	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9832572	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9834631	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9845950	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9858457	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9866535	0.81[AMR][1000 genomes]
rs9869361	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9869957	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9876771	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9877786	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1794138	chr3:136300732-136332204	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv979880	chr3:136328491-136334122	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
2	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
4	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
5	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
8	chr3:136285200-136335400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:136287200-136335400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:136289600-136341800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
15	chr3:136298600-136351600	Weak transcription	HSMM	muscle
16	chr3:136300000-136335400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:136304800-136331200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:136304800-136331400	Weak transcription	NHLF	lung
20	chr3:136305200-136339400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:136305800-136338000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:136305800-136343800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:136306000-136341400	Weak transcription	Stomach Mucosa	stomach
24	chr3:136306200-136341800	Weak transcription	Fetal Brain Female	brain
25	chr3:136306200-136343400	Weak transcription	HepG2	liver
26	chr3:136308000-136357400	Weak transcription	Lung	lung
27	chr3:136313400-136344000	Weak transcription	Fetal Heart	heart
28	chr3:136315200-136343800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:136315800-136334600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr3:136315800-136343600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:136315800-136344400	Weak transcription	Small Intestine	intestine
33	chr3:136315800-136346800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:136318400-136342000	Weak transcription	Brain Substantia Nigra	brain
38	chr3:136319000-136344000	Weak transcription	NH-A	brain
39	chr3:136319200-136336000	Weak transcription	Right Ventricle	heart
40	chr3:136319400-136336000	Weak transcription	Fetal Thymus	thymus
41	chr3:136320600-136338200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:136320600-136338200	Weak transcription	Thymus	Thymus
43	chr3:136320800-136343800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:136320800-136356800	Weak transcription	Ovary	ovary
45	chr3:136321800-136335200	Weak transcription	Osteobl	bone
46	chr3:136322000-136339200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:136322200-136331200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:136323200-136331200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:136323200-136338200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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