Variant report

Variant	rs1954435
Chromosome Location	chr9:95883363-95883364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95881490..95886849-chr9:95891631..95895235,6	K562	blood:
2	chr9:95880402..95885163-chr9:95893735..95897991,9	K562	blood:
3	chr9:95856611..95859611-chr9:95880855..95885285,4	K562	blood:
4	chr9:95856945..95860499-chr9:95877670..95883441,5	MCF-7	breast:
5	chr9:95874739..95878921-chr9:95879079..95884047,10	K562	blood:
6	chr9:95874371..95880149-chr9:95880216..95885255,14	K562	blood:

Variant related genes	Relation type
ENSG00000223446	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11792871	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	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
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	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
8	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv614879	chr9:95883363-95897564	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1954435	C9orf89	cis	parietal	SCAN
rs1954435	C9orf89	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
2	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:95871000-95894200	Weak transcription	Dnd41	blood
4	chr9:95873400-95888800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:95873600-95886000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:95874800-95883600	Weak transcription	Primary T cells from cord blood	blood
7	chr9:95876600-95886000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:95877000-95889200	Weak transcription	Fetal Brain Female	brain
9	chr9:95877200-95888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:95877400-95883800	Weak transcription	Aorta	Aorta
11	chr9:95877400-95886000	Weak transcription	Brain Germinal Matrix	brain
12	chr9:95878400-95883400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr9:95878400-95885200	Enhancers	Primary B cells from cord blood	blood
14	chr9:95879000-95884000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:95879000-95886000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:95879200-95883800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:95879200-95886000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:95879200-95886000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:95879200-95886800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:95879200-95888600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:95879200-95889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:95879400-95886000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:95881000-95884000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:95881400-95883600	Enhancers	Adipose Nuclei	Adipose
25	chr9:95881400-95883800	Enhancers	Brain Hippocampus Middle	brain
26	chr9:95881600-95883400	Enhancers	Fetal Muscle Trunk	muscle
27	chr9:95881600-95883600	Enhancers	Primary B cells from peripheral blood	blood
28	chr9:95881600-95884200	Enhancers	Primary hematopoietic stem cells	blood
29	chr9:95881800-95883400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:95881800-95883400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:95881800-95883600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr9:95881800-95883800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr9:95882000-95883400	Enhancers	Liver	Liver
34	chr9:95882000-95883800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:95882200-95883800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:95882400-95883800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr9:95882400-95888200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:95882600-95883400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:95882600-95883400	Weak transcription	Esophagus	oesophagus
40	chr9:95882600-95883400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr9:95882600-95883800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:95882600-95885000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:95882600-95887200	Weak transcription	Thymus	Thymus
44	chr9:95882600-95888600	Weak transcription	Fetal Lung	lung
45	chr9:95882600-95888600	Weak transcription	Right Atrium	heart
46	chr9:95882800-95883400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:95882800-95883400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:95882800-95883400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:95882800-95883600	Weak transcription	NHLF	lung
50	chr9:95882800-95883800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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