Variant report

Variant	rs7853552
Chromosome Location	chr9:117360797-117360798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117359468..117362349-chr9:117363469..117367925,4	K562	blood:
2	chr9:117360756..117363138-chr9:117367151..117368763,2	MCF-7	breast:
3	chr9:117357487..117362160-chr9:117372088..117375570,6	MCF-7	breast:
4	chr9:117359169..117361276-chr9:117368543..117370371,2	MCF-7	breast:
5	chr9:117358859..117360885-chr9:117367943..117371014,3	K562	blood:
6	chr9:117325612..117328013-chr9:117360752..117362499,2	K562	blood:
7	chr9:117346757..117362857-chr9:117372020..117377914,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238530	Chromatin interaction
ENSG00000157693	Chromatin interaction
ENSG00000201749	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10759725	0.82[EUR][1000 genomes]
rs10817643	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982300	1.00[CHD][hapmap]
rs10982318	1.00[CHD][hapmap]
rs10982319	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10982322	1.00[CHD][hapmap]
rs12352482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13296652	0.83[AFR][1000 genomes]
rs34424883	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
2	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
15	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised 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 miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
19	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
21	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
22	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
23	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
24	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
25	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
26	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
27	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7853552	C9orf152	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117351400-117362000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117351400-117363400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:117352000-117362400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117353600-117361600	Strong transcription	A549	lung
5	chr9:117353600-117362600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:117353600-117363400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:117353800-117360800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:117354000-117362600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:117354000-117362800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:117354200-117362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:117354200-117362400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:117354200-117363000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:117354400-117362000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:117354400-117363600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:117354400-117363800	Strong transcription	Fetal Lung	lung
16	chr9:117354600-117362600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:117354600-117363000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:117354800-117361400	Strong transcription	NH-A	brain
19	chr9:117354800-117361600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr9:117354800-117361600	Strong transcription	HepG2	liver
21	chr9:117354800-117361800	Strong transcription	HSMM	muscle
22	chr9:117354800-117362000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:117354800-117362200	Strong transcription	Fetal Brain Female	brain
24	chr9:117354800-117363000	Strong transcription	Placenta	Placenta
25	chr9:117354800-117363000	Strong transcription	Fetal Stomach	stomach
26	chr9:117354800-117363200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr9:117354800-117363200	Strong transcription	Fetal Muscle Leg	muscle
28	chr9:117354800-117363400	Strong transcription	NHLF	lung
29	chr9:117355000-117363000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:117355000-117363000	Strong transcription	Brain Germinal Matrix	brain
31	chr9:117355000-117363600	Strong transcription	Lung	lung
32	chr9:117355200-117361600	Strong transcription	Brain Anterior Caudate	brain
33	chr9:117355200-117361800	Strong transcription	Colonic Mucosa	Colon
34	chr9:117355200-117362800	Strong transcription	Brain Hippocampus Middle	brain
35	chr9:117355200-117363000	Strong transcription	Left Ventricle	heart
36	chr9:117355200-117363200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:117355400-117361800	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr9:117355400-117361800	Strong transcription	HMEC	breast
39	chr9:117355400-117362000	Strong transcription	HSMMtube	muscle
40	chr9:117355400-117362600	Strong transcription	NHEK	skin
41	chr9:117355400-117363000	Strong transcription	Esophagus	oesophagus
42	chr9:117355400-117363000	Strong transcription	Fetal Thymus	thymus
43	chr9:117355400-117363200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr9:117355400-117363200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:117355400-117363200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr9:117355400-117363400	Strong transcription	Adipose Nuclei	Adipose
47	chr9:117355400-117363400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:117355400-117363400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr9:117355400-117363400	Strong transcription	Dnd41	blood
50	chr9:117355400-117363400	Strong transcription	HUVEC	blood vessel

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