Variant report

Variant	rs28786397
Chromosome Location	chr4:107032979-107032980
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10009873	0.90[AMR][1000 genomes]
rs10010622	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10010712	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10023586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10026011	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10033060	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11544776	0.90[AMR][1000 genomes]
rs11729561	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11729801	0.90[AMR][1000 genomes]
rs11736679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28408532	0.90[AMR][1000 genomes]
rs28432701	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28472461	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28597815	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28600674	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28615207	0.90[AMR][1000 genomes]
rs28648796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663259	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28668834	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28722963	0.90[AMR][1000 genomes]
rs28783132	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28786712	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28823294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28843476	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28848568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28852980	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28857517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28890246	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6820647	0.90[AMR][1000 genomes]
rs7356173	0.90[AMR][1000 genomes]
rs7679603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7682001	0.90[AMR][1000 genomes]
rs9996386	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799793	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1801716	chr4:107000462-107062671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849248	chr4:107000462-107062671	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv1850577	chr4:107000462-107062671	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv511247	chr4:107022702-107065220	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv879701	chr4:107024776-107163128	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107012600-107033200	Weak transcription	Osteobl	bone
2	chr4:107012600-107033800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr4:107012600-107034400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:107012600-107038400	Weak transcription	NHDF-Ad	bronchial
5	chr4:107012800-107033400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:107014000-107034600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:107026200-107033600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:107026800-107035800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:107029000-107037800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:107029400-107034400	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr4:107029800-107033400	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr4:107029800-107034000	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr4:107029800-107035200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
14	chr4:107029800-107038000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:107030000-107033800	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr4:107030000-107035400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr4:107030000-107035800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr4:107030200-107033400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:107030200-107034400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr4:107030200-107036200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
21	chr4:107030400-107034000	ZNF genes & repeats	Fetal Lung	lung
22	chr4:107030600-107033800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr4:107030600-107033800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:107030600-107035200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr4:107030600-107035800	ZNF genes & repeats	Liver	Liver
26	chr4:107030800-107033400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
27	chr4:107030800-107034200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr4:107030800-107037800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:107031000-107033400	ZNF genes & repeats	Psoas Muscle	Psoas
30	chr4:107031000-107033400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
31	chr4:107031000-107033800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
32	chr4:107031000-107034000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr4:107031000-107034200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:107031000-107034200	Strong transcription	Thymus	Thymus
35	chr4:107031000-107034200	ZNF genes & repeats	HepG2	liver
36	chr4:107031000-107034400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
37	chr4:107031000-107034800	ZNF genes & repeats	Ovary	ovary
38	chr4:107031000-107036200	ZNF genes & repeats	Fetal Intestine Small	intestine
39	chr4:107031200-107033800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
40	chr4:107031200-107034000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
41	chr4:107031200-107034400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr4:107031200-107034400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr4:107031200-107034800	ZNF genes & repeats	Primary B cells from cord blood	blood
44	chr4:107031200-107035200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:107031200-107035800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr4:107031400-107034200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr4:107031600-107033200	Strong transcription	Fetal Kidney	kidney
48	chr4:107031600-107033800	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr4:107031600-107052600	Weak transcription	Fetal Thymus	thymus
50	chr4:107031800-107039400	Weak transcription	Brain Angular Gyrus	brain

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