Variant report

Variant	rs12342200
Chromosome Location	chr9:95894961-95894962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95763574..95766256-chr9:95893886..95895628,2	MCF-7	breast:
2	chr9:95870960..95873239-chr9:95894940..95897821,4	MCF-7	breast:
3	chr9:95881490..95886849-chr9:95891631..95895235,6	K562	blood:
4	chr9:95818120..95822805-chr9:95894646..95898384,4	K562	blood:
5	chr9:95525332..95528852-chr9:95893539..95896445,3	MCF-7	breast:
6	chr9:95893830..95897202-chr9:96212872..96217148,4	MCF-7	breast:
7	chr9:95892565..95895144-chr9:96051454..96053767,2	MCF-7	breast:
8	chr9:95893411..95895771-chr9:96236357..96238197,2	MCF-7	breast:
9	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:
10	chr9:95733025..95737240-chr9:95894074..95898257,5	MCF-7	breast:
11	chr9:95819594..95823966-chr9:95894549..95897415,5	MCF-7	breast:
12	chr9:95894765..95898074-chr9:96066261..96068998,4	MCF-7	breast:
13	chr9:95894803..95898160-chr9:96337820..96340366,3	MCF-7	breast:
14	chr9:95893768..95895658-chr9:95897377..95900133,3	K562	blood:
15	chr9:95894917..95896473-chr9:96212218..96213888,2	MCF-7	breast:
16	chr9:95871458..95873101-chr9:95893633..95895517,2	K562	blood:
17	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157303	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000165238	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000185963	Chromatin interaction
ENSG00000127084	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000197724	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1106192	0.84[EUR][1000 genomes]
rs12337469	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025554	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73524733	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7850887	0.81[AFR][1000 genomes]
rs7867389	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7867526	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
3	chr9:95883000-95895000	Weak transcription	K562	blood
4	chr9:95885000-95895400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:95886800-95895400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr9:95888200-95895000	Enhancers	Esophagus	oesophagus
7	chr9:95888400-95895000	Enhancers	HUVEC	blood vessel
8	chr9:95888600-95895000	Enhancers	Brain Cingulate Gyrus	brain
9	chr9:95888600-95895200	Enhancers	Left Ventricle	heart
10	chr9:95888800-95895000	Enhancers	Lung	lung
11	chr9:95889200-95895400	Weak transcription	Thymus	Thymus
12	chr9:95889400-95895000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:95889600-95895000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:95889600-95895200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:95889800-95895200	Weak transcription	Fetal Kidney	kidney
16	chr9:95890000-95895000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:95890000-95895000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:95890000-95895000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:95890000-95895000	Weak transcription	NH-A	brain
20	chr9:95890000-95895600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr9:95890400-95896600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:95890800-95896000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr9:95891400-95895800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr9:95892400-95895200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:95892600-95895000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:95892600-95895200	Enhancers	Fetal Thymus	thymus
27	chr9:95892800-95895000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr9:95892800-95895000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:95892800-95895800	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr9:95893000-95895000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:95893000-95895000	Enhancers	Ovary	ovary
32	chr9:95893000-95895200	Enhancers	Fetal Lung	lung
33	chr9:95893000-95896200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr9:95893200-95895400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:95893200-95896000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:95893200-95896000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr9:95893200-95896000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr9:95893200-95896000	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr9:95893400-95895000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:95893400-95895000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:95893400-95895200	Enhancers	Gastric	stomach
42	chr9:95893400-95895800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr9:95893600-95895000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:95893600-95895200	Enhancers	Right Ventricle	heart
45	chr9:95893600-95895600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:95893600-95895600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr9:95893600-95895800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr9:95893800-95895000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr9:95893800-95895400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:95893800-95895600	Enhancers	Sigmoid Colon	Sigmoid Colon

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