Variant report

Variant	rs28408532
Chromosome Location	chr4:107228745-107228746
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:107226289..107231817-chr4:107234990..107238909,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145348	Chromatin interaction
ENSG00000164022	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10009873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10010622	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10010712	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10026011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10033060	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11544776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11729801	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11736679	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28432701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28597815	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28600674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28615207	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28648796	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28668834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28722963	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28783132	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28786397	0.90[AMR][1000 genomes]
rs28786712	0.90[AMR][1000 genomes]
rs28823294	0.90[AMR][1000 genomes]
rs28843476	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28848568	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28852980	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28857517	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs28890246	0.90[AMR][1000 genomes]
rs6820647	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7356173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7682001	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9996386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1819960	chr4:107216320-107246136	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107114600-107236000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:107155600-107236000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:107178000-107236200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:107178000-107236200	Weak transcription	Right Ventricle	heart
5	chr4:107178000-107236600	Weak transcription	Esophagus	oesophagus
6	chr4:107178000-107236600	Weak transcription	Pancreas	Pancrea
7	chr4:107178200-107236000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:107198800-107235600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:107202800-107236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:107204000-107235800	Weak transcription	Psoas Muscle	Psoas
11	chr4:107204000-107236200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr4:107205600-107236000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:107208000-107229600	Weak transcription	Aorta	Aorta
14	chr4:107209000-107229400	Weak transcription	GM12878-XiMat	blood
15	chr4:107209000-107231200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:107209200-107236000	Weak transcription	HMEC	breast
17	chr4:107212200-107234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:107213200-107235600	Weak transcription	Fetal Kidney	kidney
19	chr4:107213200-107236200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:107213400-107236000	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:107213400-107236200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:107215600-107236000	Weak transcription	Brain Germinal Matrix	brain
23	chr4:107215600-107236200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:107215800-107229600	Weak transcription	Dnd41	blood
25	chr4:107215800-107236600	Weak transcription	Small Intestine	intestine
26	chr4:107215800-107236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:107216000-107235600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:107216200-107229200	Weak transcription	Fetal Lung	lung
29	chr4:107216200-107236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:107216200-107236200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:107216200-107236200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:107216400-107229400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:107216400-107229600	Weak transcription	Gastric	stomach
34	chr4:107216400-107233800	Weak transcription	NH-A	brain
35	chr4:107216400-107235200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:107216400-107236000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr4:107216400-107236200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:107216400-107236200	Weak transcription	Thymus	Thymus
39	chr4:107216400-107236600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:107217000-107229200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:107217800-107236000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:107218800-107236200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:107220200-107235600	Weak transcription	Fetal Brain Male	brain
44	chr4:107220400-107229600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:107221200-107236000	Weak transcription	Placenta	Placenta
46	chr4:107221200-107236000	Weak transcription	HUVEC	blood vessel
47	chr4:107221200-107236600	Weak transcription	Left Ventricle	heart
48	chr4:107221400-107229400	Weak transcription	Lung	lung
49	chr4:107221400-107234200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr4:107221400-107236000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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