Variant report

Variant	rs7039638
Chromosome Location	chr9:108007947-108007948
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26031886..26032421-chr9:108007272..108008250,2	Hela-S3	cervix:
2	chr9:108006963..108009238-chr9:108022447..108024092,2	MCF-7	breast:
3	chr9:107964013..107966115-chr9:108007069..108009049,2	MCF-7	breast:
4	chr9:107986434..107988530-chr9:108007277..108010113,2	MCF-7	breast:
5	chr9:108007121..108007988-chr9:108175578..108176396,3	MCF-7	breast:
6	chr9:107948857..107951560-chr9:108005097..108008240,3	MCF-7	breast:
7	chr9:108007148..108008877-chr9:108174581..108177913,4	MCF-7	breast:
8	chr9:108006964..108008816-chr9:108165166..108168105,2	MCF-7	breast:
9	chr9:108005738..108008360-chr9:108117762..108120177,2	MCF-7	breast:
10	chr9:108007022..108007998-chr9:108122682..108123316,3	MCF-7	breast:
11	chr9:108007262..108007998-chr9:108175454..108176410,3	MCF-7	breast:
12	chr9:107687369..107691649-chr9:108006197..108009884,7	MCF-7	breast:
13	chr9:108007303..108009573-chr9:108053805..108056055,2	MCF-7	breast:
14	chr9:107904194..107906765-chr9:108007305..108010272,2	MCF-7	breast:
15	chr9:108003331..108004862-chr9:108007062..108008730,2	MCF-7	breast:
16	chr9:107631539..107633067-chr9:108007173..108009446,2	MCF-7	breast:
17	chr9:108006932..108009449-chr9:108036462..108038843,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000238208	Chromatin interaction
ENSG00000070214	Chromatin interaction
ENSG00000165029	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000226334	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12341869	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688962	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57877883	1.00[AMR][1000 genomes]
rs59290851	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479300	0.98[AFR][1000 genomes]
rs6479301	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479302	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479303	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7024012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7033929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046185	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7048497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72744219	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72744225	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510211	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510280	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510289	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510295	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666624	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666625	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847744	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847952	0.92[AFR][1000 genomes]
rs7853038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853709	0.83[AMR][1000 genomes]
rs7854064	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854282	1.00[AMR][1000 genomes]
rs7857088	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7860356	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7869261	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7873924	0.83[AMR][1000 genomes]
rs7874307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9777083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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
6	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	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
9	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893691	chr9:107994629-108020284	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3368118	chr9:108006181-108008254	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108004800-108009400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr9:108005000-108009200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:108006000-108008000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:108006000-108008400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr9:108006000-108008600	Active TSS	A549	lung
6	chr9:108006200-108008000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:108006200-108008000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:108006200-108008200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr9:108006200-108008200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:108006200-108008200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:108006200-108008200	Active TSS	Colon Smooth Muscle	Colon
12	chr9:108006200-108008200	Active TSS	Esophagus	oesophagus
13	chr9:108006200-108008200	Active TSS	Placenta Amnion	Placenta Amnion
14	chr9:108006200-108008200	Active TSS	HSMMtube	muscle
15	chr9:108006200-108008400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:108006200-108008400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:108006200-108008400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:108006200-108008400	Active TSS	Left Ventricle	heart
19	chr9:108006200-108008400	Active TSS	Stomach Smooth Muscle	stomach
20	chr9:108006200-108008600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr9:108006200-108008600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:108006200-108008600	Active TSS	Ovary	ovary
23	chr9:108006200-108008600	Active TSS	Psoas Muscle	Psoas
24	chr9:108006200-108009000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr9:108006200-108009000	Active TSS	Aorta	Aorta
26	chr9:108006200-108009000	Active TSS	Brain Germinal Matrix	brain
27	chr9:108006200-108009000	Active TSS	Duodenum Mucosa	Duodenum
28	chr9:108006200-108009200	Active TSS	Right Atrium	heart
29	chr9:108006200-108009600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:108006200-108010000	Active TSS	Brain Cingulate Gyrus	brain
31	chr9:108006200-108010400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:108006200-108011800	Active TSS	Brain Hippocampus Middle	brain
33	chr9:108006400-108008000	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr9:108006400-108008000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr9:108006400-108008000	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr9:108006400-108008000	Active TSS	NHLF	lung
37	chr9:108006400-108008200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:108006400-108008200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:108006400-108008200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:108006400-108008200	Active TSS	Gastric	stomach
41	chr9:108006400-108008200	Active TSS	Pancreas	Pancrea
42	chr9:108006400-108008400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:108006400-108008400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr9:108006400-108008400	Active TSS	Fetal Intestine Small	intestine
45	chr9:108006400-108008400	Active TSS	Lung	lung
46	chr9:108006400-108008400	Active TSS	Small Intestine	intestine
47	chr9:108006400-108008600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr9:108006400-108008600	Active TSS	Colonic Mucosa	Colon
49	chr9:108006400-108008600	Active TSS	Fetal Kidney	kidney
50	chr9:108006400-108008600	Active TSS	Fetal Lung	lung

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