Variant report

Variant	rs28564406
Chromosome Location	chr9:100977120-100977121
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100976860..100978461-chr9:101017333..101019221,2	MCF-7	breast:
2	chr9:100879928..100882828-chr9:100976182..100978819,2	MCF-7	breast:
3	chr9:100818654..100820478-chr9:100976673..100978536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095383	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10122936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10985471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11788019	1.00[EUR][1000 genomes]
rs28504114	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28549704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55754658	0.94[AFR][1000 genomes]
rs55866532	1.00[EUR][1000 genomes]
rs7040214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7854249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:100956000-100981000	Weak transcription	A549	lung
3	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:100959600-100984400	Strong transcription	Osteobl	bone
5	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
7	chr9:100965600-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:100968000-100987000	Weak transcription	Small Intestine	intestine
9	chr9:100968400-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:100968600-100985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:100968800-100984600	Weak transcription	K562	blood
15	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr9:100969000-100979000	Weak transcription	Fetal Brain Female	brain
18	chr9:100969000-100984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:100969200-100985600	Strong transcription	Fetal Intestine Small	intestine
20	chr9:100969400-100980600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:100969400-100981000	Strong transcription	Placenta	Placenta
22	chr9:100969400-100981000	Weak transcription	Fetal Thymus	thymus
23	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
24	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:100969800-100977800	Strong transcription	Primary T cells from cord blood	blood
26	chr9:100969800-100991800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:100970000-100985400	Strong transcription	Spleen	Spleen
28	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:100970400-100983800	Strong transcription	HSMMtube	muscle
30	chr9:100970600-100977200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:100971200-100977400	Weak transcription	Brain Angular Gyrus	brain
32	chr9:100971200-100977800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:100971200-100981000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:100971200-100981800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:100971200-100985200	Strong transcription	Lung	lung
36	chr9:100971400-100979600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:100971400-100982200	Weak transcription	Ovary	ovary
38	chr9:100971400-100985400	Strong transcription	Fetal Intestine Large	intestine
39	chr9:100971600-100979800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:100971600-100981000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr9:100971600-100982000	Weak transcription	Pancreas	Pancrea
42	chr9:100972400-100983800	Strong transcription	HSMM	muscle
43	chr9:100973000-100977400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:100973000-100981800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:100973000-100985800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:100973200-100979200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:100973200-100981600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:100973400-100978200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr9:100973600-100980400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:100973800-100985400	Weak transcription	Stomach Mucosa	stomach

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