Variant report

Variant	rs28545469
Chromosome Location	chr9:108091643-108091644
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	chr9:108006187..108008080-chr9:108090589..108092935,2	K562	blood:
2	chr9:108006762..108008721-chr9:108091496..108094176,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10081709	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10115833	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10115879	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10116656	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10820799	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10820800	0.83[AFR][1000 genomes]
rs10991624	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10991628	0.84[AFR][1000 genomes]
rs10991629	0.82[AFR][1000 genomes]
rs11506819	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339205	1.00[EUR][1000 genomes]
rs12348983	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12350341	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13289885	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13297419	1.00[EUR][1000 genomes]
rs13298325	1.00[EUR][1000 genomes]
rs13299711	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924487	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2417614	0.85[AFR][1000 genomes]
rs34253461	1.00[EUR][1000 genomes]
rs34331578	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34350840	1.00[EUR][1000 genomes]
rs35111325	1.00[EUR][1000 genomes]
rs35275407	1.00[EUR][1000 genomes]
rs35322610	1.00[EUR][1000 genomes]
rs35533765	1.00[EUR][1000 genomes]
rs60502553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479309	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67844420	1.00[EUR][1000 genomes]
rs7034136	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7040751	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048586	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71494522	0.88[EUR][1000 genomes]
rs71494524	1.00[EUR][1000 genomes]
rs71494526	1.00[EUR][1000 genomes]
rs71494527	1.00[EUR][1000 genomes]
rs7856033	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7856524	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860321	1.00[EUR][1000 genomes]
rs7863414	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7863781	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7870687	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7871855	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7873937	0.87[AFR][1000 genomes]
rs9299385	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299386	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299387	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs932006	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9632901	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108062200-108091800	Weak transcription	Aorta	Aorta
3	chr9:108062200-108098800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr9:108062400-108098800	Weak transcription	Spleen	Spleen
5	chr9:108062400-108104600	Weak transcription	Right Ventricle	heart
6	chr9:108062600-108098600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:108062600-108098800	Weak transcription	Left Ventricle	heart
8	chr9:108062600-108098800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:108062800-108098400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:108062800-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:108066200-108098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:108068800-108098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr9:108069000-108104000	Weak transcription	Fetal Heart	heart
14	chr9:108070400-108091800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:108070400-108093400	Weak transcription	Gastric	stomach
16	chr9:108070400-108094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:108071600-108099000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:108071800-108097800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:108072400-108094200	Weak transcription	HSMM	muscle
20	chr9:108072400-108098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:108072600-108094800	Weak transcription	HSMMtube	muscle
22	chr9:108076000-108096200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:108078400-108101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:108079600-108098800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:108080000-108098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:108080400-108097800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
28	chr9:108081600-108096400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr9:108081800-108091800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:108082000-108091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:108082000-108097600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:108082000-108098800	Weak transcription	Pancreas	Pancrea
33	chr9:108082200-108098600	Weak transcription	Primary T cells from cord blood	blood
34	chr9:108083200-108092000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:108083600-108092400	Weak transcription	Liver	Liver
36	chr9:108083800-108092000	Weak transcription	A549	lung
37	chr9:108084800-108091800	Weak transcription	Stomach Mucosa	stomach
38	chr9:108085000-108092000	Weak transcription	Fetal Intestine Large	intestine
39	chr9:108085000-108097800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr9:108085400-108092000	Weak transcription	Fetal Intestine Small	intestine
41	chr9:108085800-108092400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:108087400-108098600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:108087600-108091800	Weak transcription	Fetal Lung	lung
44	chr9:108088400-108094800	Weak transcription	NH-A	brain
45	chr9:108089000-108092400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:108089600-108097600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:108090000-108097800	Enhancers	Brain Substantia Nigra	brain
48	chr9:108090000-108098800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:108090200-108091800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr9:108090400-108092400	Enhancers	HUES64 Cell Line	embryonic stem cell

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