Variant report

Variant	rs28549704
Chromosome Location	chr9:100974343-100974344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100971993..100974681-chr9:101050023..101052189,2	MCF-7	breast:
2	chr9:100973089..100975981-chr9:101016778..101019724,3	MCF-7	breast:
3	chr9:100951009..100953373-chr9:100973381..100975463,2	K562	blood:
4	chr9:100966722..100970039-chr9:100971164..100974446,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000095383	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];0.85[EUR][1000 genomes]
rs10985471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11788019	0.85[EUR][1000 genomes]
rs28504114	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28564406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55754658	0.94[AFR][1000 genomes]
rs55866532	0.85[EUR][1000 genomes]
rs7040214	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7854249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-100975000	Weak transcription	Primary B cells from cord blood	blood
2	chr9:100955800-100975000	Weak transcription	NHDF-Ad	bronchial
3	chr9:100955800-100975200	Weak transcription	NH-A	brain
4	chr9:100955800-100975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:100956000-100981000	Weak transcription	A549	lung
7	chr9:100958600-100985400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr9:100959200-100977000	Strong transcription	HMEC	breast
9	chr9:100959600-100984400	Strong transcription	Osteobl	bone
10	chr9:100959800-100985200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
12	chr9:100962600-100975200	Weak transcription	Brain Anterior Caudate	brain
13	chr9:100965600-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:100968000-100987000	Weak transcription	Small Intestine	intestine
15	chr9:100968200-100976400	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr9:100968400-100982200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr9:100968600-100985400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:100968800-100975200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr9:100968800-100984600	Weak transcription	K562	blood
23	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr9:100969000-100979000	Weak transcription	Fetal Brain Female	brain
26	chr9:100969000-100984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:100969200-100976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:100969200-100985600	Strong transcription	Fetal Intestine Small	intestine
29	chr9:100969400-100980600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:100969400-100981000	Strong transcription	Placenta	Placenta
31	chr9:100969400-100981000	Weak transcription	Fetal Thymus	thymus
32	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
33	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:100969800-100975600	Strong transcription	Brain Hippocampus Middle	brain
35	chr9:100969800-100977000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:100969800-100977800	Strong transcription	Primary T cells from cord blood	blood
37	chr9:100969800-100991800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr9:100970000-100974600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr9:100970000-100985400	Strong transcription	Spleen	Spleen
40	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr9:100970400-100975400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:100970400-100976200	Strong transcription	NHLF	lung
43	chr9:100970400-100983800	Strong transcription	HSMMtube	muscle
44	chr9:100970600-100977200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:100970800-100976200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:100970800-100977000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:100971000-100975200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:100971000-100975200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:100971000-100975400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:100971000-100977000	Strong transcription	NHEK	skin

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