Variant report

Variant	rs12552323
Chromosome Location	chr9:96442814-96442815
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96442742..96446259-chr9:96719078..96722660,3	MCF-7	breast:
2	chr9:96338337..96340643-chr9:96441518..96443236,3	MCF-7	breast:
3	chr9:96382332..96382997-chr9:96442806..96443414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197724	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10992845	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1132027	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12551079	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12551694	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12553909	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12555927	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17532098	0.85[CEU][hapmap]
rs17535326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2001609	0.82[CEU][hapmap]
rs3813386	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3829059	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3893381	1.00[ASW][hapmap]
rs55783552	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56310424	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7033532	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7038293	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7038310	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7038794	0.81[EUR][1000 genomes]
rs883783	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:96412800-96443600	Weak transcription	Stomach Mucosa	stomach
3	chr9:96413000-96444800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:96416400-96443400	Weak transcription	HepG2	liver
5	chr9:96434600-96443200	Strong transcription	Fetal Stomach	stomach
6	chr9:96436600-96443800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:96436800-96447000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:96437800-96444800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:96438800-96443800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:96439600-96443200	Weak transcription	Psoas Muscle	Psoas
11	chr9:96439600-96444800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:96439800-96444800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:96439800-96444800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:96440200-96444400	Weak transcription	A549	lung
15	chr9:96440400-96443000	Weak transcription	HSMMtube	muscle
16	chr9:96440400-96444000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:96440400-96444200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:96440400-96444400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:96440400-96444800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:96440600-96443400	Weak transcription	Small Intestine	intestine
21	chr9:96440600-96443800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:96440600-96444000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:96440600-96444400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr9:96440600-96444600	Weak transcription	Fetal Lung	lung
25	chr9:96440600-96444800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:96440600-96447600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:96440800-96443000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:96440800-96443200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:96440800-96443600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:96440800-96443600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:96440800-96443600	Weak transcription	Liver	Liver
32	chr9:96440800-96443600	Weak transcription	Gastric	stomach
33	chr9:96440800-96443800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:96440800-96443800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:96440800-96444000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:96440800-96444200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:96440800-96444400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr9:96440800-96444400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr9:96440800-96444600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:96440800-96444800	Weak transcription	Left Ventricle	heart
41	chr9:96440800-96445600	Weak transcription	NHLF	lung
42	chr9:96440800-96447400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:96441000-96443800	Weak transcription	Pancreas	Pancrea
44	chr9:96441000-96444000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr9:96441000-96444000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:96441000-96444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:96441000-96444200	Weak transcription	Esophagus	oesophagus
48	chr9:96441000-96444400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:96441000-96446400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:96441000-96447200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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