Variant report

Variant	rs28635946
Chromosome Location	chr9:100954582-100954583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100939196..100942358-chr9:100952088..100954820,4	MCF-7	breast:
2	chr9:100817834..100821135-chr9:100954026..100958556,6	MCF-7	breast:
3	chr9:100952914..100958060-chr9:101016344..101019894,9	MCF-7	breast:
4	chr9:100880793..100881841-chr9:100954446..100955221,3	MCF-7	breast:
5	chr9:100951866..100957184-chr9:101014234..101020511,10	K562	blood:
6	chr9:100932527..100936703-chr9:100952110..100957364,6	MCF-7	breast:
7	chr9:100952199..100954695-chr9:100957518..100959122,2	K562	blood:
8	chr9:100880445..100882322-chr9:100953652..100955695,2	K562	blood:
9	chr9:100880288..100886270-chr9:100953608..100957100,8	MCF-7	breast:
10	chr9:100746284..100748016-chr9:100953069..100955569,2	MCF-7	breast:
11	chr9:100835251..100838541-chr9:100953348..100956508,6	MCF-7	breast:
12	chr9:100877974..100882322-chr9:100953652..100957621,5	K562	blood:
13	chr9:100934419..100936711-chr9:100950978..100955014,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106785	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000106789	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12001270	0.82[EUR][1000 genomes]
rs12344498	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12344678	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12349129	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12349172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16913609	0.84[EUR][1000 genomes]
rs55710345	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56350443	0.82[EUR][1000 genomes]
rs56675709	0.82[EUR][1000 genomes]
rs57756870	0.82[EUR][1000 genomes]
rs57761120	0.84[EUR][1000 genomes]
rs58302299	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs58653026	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58762276	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs60887768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7033797	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs73498781	0.82[EUR][1000 genomes]
rs73498784	0.82[EUR][1000 genomes]
rs73503038	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73657117	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3415002	chr9:100953931-100956079	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100953200-100954600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:100953200-100955400	Active TSS	Esophagus	oesophagus
3	chr9:100953200-100955600	Active TSS	Gastric	stomach
4	chr9:100953400-100954800	Flanking Active TSS	Colonic Mucosa	Colon
5	chr9:100953600-100954600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr9:100953600-100954600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr9:100953600-100954600	Enhancers	Fetal Brain Male	brain
8	chr9:100953600-100954800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:100953600-100955400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:100953600-100955600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr9:100953600-100955800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:100953600-100955800	Active TSS	Rectal Smooth Muscle	rectum
13	chr9:100953800-100954600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr9:100953800-100954600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr9:100953800-100954600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr9:100953800-100954600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:100953800-100954600	Flanking Active TSS	Thymus	Thymus
18	chr9:100953800-100954800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:100953800-100954800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
20	chr9:100953800-100954800	Flanking Active TSS	Dnd41	blood
21	chr9:100953800-100955400	Active TSS	Fetal Intestine Small	intestine
22	chr9:100953800-100955800	Flanking Active TSS	HMEC	breast
23	chr9:100953800-100956000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr9:100954000-100954600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr9:100954000-100954600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr9:100954000-100954600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:100954000-100954600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr9:100954000-100954600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:100954000-100954600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr9:100954000-100954600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr9:100954000-100954800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:100954000-100954800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:100954000-100954800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
34	chr9:100954000-100954800	Flanking Active TSS	Fetal Thymus	thymus
35	chr9:100954000-100955000	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr9:100954000-100955400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:100954000-100955400	Active TSS	Placenta Amnion	Placenta Amnion
38	chr9:100954000-100955600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr9:100954000-100955600	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr9:100954000-100955600	Active TSS	Stomach Mucosa	stomach
41	chr9:100954000-100955600	Active TSS	A549	lung
42	chr9:100954000-100955800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr9:100954000-100955800	Active TSS	Right Ventricle	heart
44	chr9:100954000-100956000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:100954000-100956000	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr9:100954000-100956000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr9:100954200-100954600	Flanking Bivalent TSS/Enh	Placenta	Placenta
48	chr9:100954200-100954600	Flanking Active TSS	Lung	lung
49	chr9:100954200-100954600	Flanking Active TSS	Spleen	Spleen
50	chr9:100954200-100954800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood

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