Variant report

Variant	rs11089447
Chromosome Location	chr22:30794719-30794720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:30793321-30795253	Raji	blood:	n/a	n/a
2	POLR2A	chr22:30794232-30795083	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr22:30793524-30795326	PBDE	blood:	n/a	n/a
4	POLR2A	chr22:30791787-30796585	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:30792617-30795297	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:30792819-30795221	Hela-S3	cervix:	n/a	n/a
7	E2F4	chr22:30794482-30794910	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr22:30793918-30795516	HepG2	liver:	n/a	n/a
9	POLR2A	chr22:30794473-30795298	GM12878	blood:	n/a	n/a
10	POLR2A	chr22:30792640-30795327	K562	blood:	n/a	n/a
11	POLR2A	chr22:30794186-30794980	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30787731..30797808-chr22:30813672..30825727,31	MCF-7	breast:
2	chr22:30793027..30795107-chr22:30817004..30819701,2	K562	blood:
3	chr17:56736502..56738510-chr22:30792727..30794981,2	MCF-7	breast:
4	chr22:30791754..30798377-chr22:30814746..30822334,13	K562	blood:

No data

Variant related genes	Relation type
SEC14L2	TF binding region
ENSG00000273350	Chromatin interaction
ENSG00000242114	Chromatin interaction
ENSG00000099999	Chromatin interaction
ENSG00000268538	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000272689	Chromatin interaction
ENSG00000222915	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1005835	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1010324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11089442	0.82[CEU][hapmap]
rs11089448	0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11089449	0.83[AMR][1000 genomes]
rs11703867	0.83[AMR][1000 genomes]
rs11705639	0.81[AMR][1000 genomes]
rs12171261	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2072160	0.86[AMR][1000 genomes]
rs2074731	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs2267154	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2267155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2267156	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2283866	0.84[AMR][1000 genomes]
rs2283870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2283871	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2299827	0.92[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2839998	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs57940170	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5994294	0.91[CEU][hapmap];0.85[AMR][1000 genomes]
rs5994305	0.85[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes]
rs5994306	0.86[AMR][1000 genomes]
rs5997637	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs5997646	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs61583714	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71331235	0.85[AMR][1000 genomes]
rs7288366	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7289360	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7290317	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8141656	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs9619096	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs9619098	0.85[AMR][1000 genomes]
rs9619105	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9620984	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11089447	SYN3	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30792600-30794800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr22:30792600-30795400	Enhancers	Spleen	Spleen
3	chr22:30792800-30794800	Active TSS	HSMMtube	muscle
4	chr22:30792800-30795000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr22:30792800-30795600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:30793200-30794800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr22:30793400-30794800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr22:30793400-30794800	Flanking Active TSS	Thymus	Thymus
9	chr22:30793400-30795000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr22:30793400-30795200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr22:30793400-30795400	Flanking Active TSS	Dnd41	blood
12	chr22:30793600-30794800	Flanking Active TSS	Esophagus	oesophagus
13	chr22:30793600-30794800	Bivalent Enhancer	Placenta	Placenta
14	chr22:30793600-30794800	Flanking Active TSS	Hela-S3	cervix
15	chr22:30793600-30795000	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr22:30793600-30795000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr22:30793600-30795000	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr22:30793600-30795000	Flanking Active TSS	Brain Substantia Nigra	brain
19	chr22:30793600-30795000	Flanking Active TSS	Osteobl	bone
20	chr22:30793600-30795200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr22:30793600-30795200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:30793600-30795200	Enhancers	K562	blood
23	chr22:30793600-30795200	Flanking Active TSS	NH-A	brain
24	chr22:30793600-30795400	Flanking Active TSS	Liver	Liver
25	chr22:30793600-30795400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr22:30793800-30794800	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr22:30793800-30794800	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr22:30793800-30794800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
29	chr22:30793800-30795200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:30793800-30795200	Enhancers	Pancreas	Pancrea
31	chr22:30793800-30795400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr22:30794000-30794800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr22:30794000-30794800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
34	chr22:30794000-30794800	Flanking Active TSS	HepG2	liver
35	chr22:30794000-30795000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr22:30794000-30795000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr22:30794000-30795000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:30794000-30795000	Bivalent Enhancer	Adipose Nuclei	Adipose
39	chr22:30794000-30795000	Enhancers	Fetal Lung	lung
40	chr22:30794000-30795200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr22:30794000-30795200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:30794000-30795200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr22:30794000-30795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr22:30794000-30795200	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr22:30794000-30795200	Enhancers	Ovary	ovary
46	chr22:30794000-30795200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr22:30794000-30795200	Enhancers	Small Intestine	intestine
48	chr22:30794000-30816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr22:30794000-30818000	Weak transcription	Right Atrium	heart
50	chr22:30794200-30794800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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