Variant report

Variant	rs7858616
Chromosome Location	chr9:108277604-108277605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10991682	0.94[AFR][1000 genomes]
rs11999966	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12002748	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12004019	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12004886	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12342071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13362922	0.83[AFR][1000 genomes]
rs1808155	0.97[AFR][1000 genomes]
rs1854124	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2149592	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2149593	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2417627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41277781	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66820447	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7033452	0.97[AFR][1000 genomes]
rs7034699	0.95[AFR][1000 genomes]
rs7034702	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7042000	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7867012	0.96[AFR][1000 genomes]
rs7870485	0.87[AFR][1000 genomes]
rs9657645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
2	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
3	chr9:108227600-108278400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr9:108231800-108296800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:108242600-108300000	Weak transcription	Brain Anterior Caudate	brain
6	chr9:108258200-108282000	Weak transcription	Psoas Muscle	Psoas
7	chr9:108259600-108282000	Weak transcription	HSMMtube	muscle
8	chr9:108266400-108277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:108266600-108278000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:108266600-108278000	Weak transcription	K562	blood
11	chr9:108266600-108282000	Weak transcription	Hela-S3	cervix
12	chr9:108266800-108277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:108268200-108279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:108268200-108279600	Weak transcription	Fetal Kidney	kidney
15	chr9:108268200-108306000	Weak transcription	Brain Angular Gyrus	brain
16	chr9:108269200-108282000	Weak transcription	Pancreas	Pancrea
17	chr9:108269400-108280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:108269800-108282000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:108269800-108286200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:108270800-108280200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:108271200-108280200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:108272600-108282000	Weak transcription	Gastric	stomach
23	chr9:108272800-108282400	Weak transcription	NHLF	lung
24	chr9:108272800-108304600	Weak transcription	NHEK	skin
25	chr9:108273000-108282000	Weak transcription	HSMM	muscle
26	chr9:108273000-108282000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr9:108273000-108282200	Weak transcription	NH-A	brain
28	chr9:108273000-108282200	Weak transcription	NHDF-Ad	bronchial
29	chr9:108274200-108278000	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:108274200-108278200	Weak transcription	Brain Substantia Nigra	brain
31	chr9:108274200-108279400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:108274400-108277800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:108274400-108299800	Weak transcription	Fetal Lung	lung
34	chr9:108275200-108278000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:108275200-108279000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:108275200-108282000	Weak transcription	Esophagus	oesophagus
37	chr9:108275400-108279000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:108275400-108279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:108276000-108279200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:108276000-108282000	Weak transcription	Osteobl	bone
41	chr9:108276200-108277800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:108276200-108278800	ZNF genes & repeats	GM12878-XiMat	blood
43	chr9:108276200-108309200	Weak transcription	Lung	lung
44	chr9:108276400-108282000	Weak transcription	Spleen	Spleen
45	chr9:108276600-108279600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:108276800-108278000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr9:108276800-108278200	Strong transcription	Fetal Brain Female	brain
48	chr9:108276800-108278400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:108276800-108278800	Strong transcription	A549	lung
50	chr9:108276800-108279200	Strong transcription	Brain Germinal Matrix	brain

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