Variant report

Variant	rs2398820
Chromosome Location	chr9:95996573-95996574
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12341303	0.81[GIH][hapmap]
rs4744195	0.81[GIH][hapmap]

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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2398820	C9orf89	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95984800-95998000	Enhancers	Pancreas	Pancrea
2	chr9:95986200-96006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:95987200-95996800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:95987200-95997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:95987200-96000200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:95987400-96001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:95987400-96005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:95988200-96006800	Weak transcription	Esophagus	oesophagus
9	chr9:95988400-95999800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:95988600-95997200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:95992200-95999800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:95993600-95997600	Weak transcription	Fetal Lung	lung
13	chr9:95993600-96005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:95993800-95997400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:95993800-96001800	Weak transcription	Spleen	Spleen
16	chr9:95994000-95997200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:95994000-95997400	Weak transcription	Fetal Heart	heart
18	chr9:95994000-96001000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:95994200-95996800	Weak transcription	Right Ventricle	heart
20	chr9:95994200-95997200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:95994400-95997200	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:95994600-95997400	Weak transcription	Brain Substantia Nigra	brain
23	chr9:95994600-95997600	Weak transcription	Gastric	stomach
24	chr9:95994800-95996800	Weak transcription	Brain Germinal Matrix	brain
25	chr9:95994800-95997000	Weak transcription	Brain Angular Gyrus	brain
26	chr9:95994800-95997000	Weak transcription	HepG2	liver
27	chr9:95994800-95997400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:95995000-95996600	Weak transcription	Left Ventricle	heart
29	chr9:95995000-95996800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:95995000-95996800	Weak transcription	Colonic Mucosa	Colon
31	chr9:95995200-95996600	Weak transcription	Psoas Muscle	Psoas
32	chr9:95995200-95997400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:95995200-96000600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:95995400-95997800	Strong transcription	Fetal Intestine Small	intestine
36	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:95996200-95997000	Enhancers	Fetal Stomach	stomach
38	chr9:95996200-95998000	Strong transcription	Fetal Intestine Large	intestine
39	chr9:95996200-95999200	Enhancers	Stomach Mucosa	stomach
40	chr9:95996200-95999400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr9:95996200-96001200	Genic enhancers	Rectal Mucosa Donor 31	rectum
42	chr9:95996400-95997000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr9:95996400-95997000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr9:95996400-95997200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:95996400-95998800	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr9:95996400-95999000	Enhancers	Fetal Muscle Leg	muscle
47	chr9:95996400-95999200	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr9:95996400-95999400	Enhancers	Placenta	Placenta
49	chr9:95996400-96004400	Strong transcription	Fetal Brain Female	brain
50	chr9:95996400-96011200	Strong transcription	Stomach Smooth Muscle	stomach

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