Variant report

Variant	rs11168953
Chromosome Location	chr12:49661914-49661915
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49658351-49664605	U87	brain:	n/a	n/a
2	POLR2A	chr12:49661335-49662059	U87	brain:	n/a	n/a
3	POLR2A	chr12:49660160-49662050	K562	blood:	n/a	n/a
4	POLR2A	chr12:49658001-49664653	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
6	POLR2A	chr12:49658069-49662113	K562	blood:	n/a	n/a
7	HEY1	chr12:49661800-49662000	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:49660207-49662000	K562	blood:	n/a	n/a
9	POLR2A	chr12:49660119-49662037	K562	blood:	n/a	n/a
10	POLR2A	chr12:49661341-49662112	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr12:49657881-49662104	U87	brain:	n/a	n/a
12	POLR2A	chr12:49657892-49662191	SK-N-MC	brain:	n/a	n/a
13	HEY1	chr12:49660069-49662204	K562	blood:	n/a	n/a
14	POLR2A	chr12:49660147-49662192	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:49661341-49661996	U87	brain:	n/a	n/a
16	POLR2A	chr12:49661358-49662763	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr12:49661272-49662002	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr12:49661863-49662027	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:49658134-49662185	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:49660999-49662720	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:49658512-49661970	K562	blood:	n/a	n/a
23	POLR2A	chr12:49661890-49661964	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:49660140-49661968	K562	blood:	n/a	n/a
25	POLR2A	chr12:49660135-49662199	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:49661754-49662118	K562	blood:	n/a	n/a
27	POLR2A	chr12:49658744-49662063	A549	lung:	n/a	n/a
28	POLR2A	chr12:49661244-49662053	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr12:49657200-49661932	PANC-1	pancreas:	n/a	n/a
30	BCLAF1	chr12:49660092-49662012	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49656742..49663815-chr12:49736558..49745017,19	MCF-7	breast:
2	chr12:49523107..49527860-chr12:49656151..49664210,14	MCF-7	breast:
3	chr12:49519590..49527322-chr12:49655772..49662610,57	K562	blood:
4	chr12:49660606..49662503-chr12:62995463..62997195,2	MCF-7	breast:
5	chr12:49533073..49535795-chr12:49661700..49663392,2	K562	blood:
6	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
7	chr12:49661105..49664061-chr17:56709024..56710621,2	MCF-7	breast:
8	chr12:49519914..49528393-chr12:49656527..49662615,75	K562	blood:
9	chr12:49628076..49629914-chr12:49660607..49662737,2	MCF-7	breast:
10	chr12:49619902..49623805-chr12:49655877..49662372,6	K562	blood:
11	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
12	chr12:49660927..49665723-chr12:49685096..49688729,4	MCF-7	breast:
13	chr12:49656722..49663896-chr12:49682381..49687774,8	K562	blood:
14	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
15	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
16	chr12:49500184..49504763-chr12:49658087..49663330,8	K562	blood:
17	chr12:49657182..49662198-chr12:49738070..49742868,13	MCF-7	breast:
18	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
19	chr12:49483859..49489908-chr12:49657302..49662649,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258101	TF binding region
TUBA1C	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000257354	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000139549	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11168952	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168955	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168956	0.82[AFR][1000 genomes]
rs11168957	0.82[AFR][1000 genomes]
rs11168958	0.82[AFR][1000 genomes]
rs11542115	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308571	0.82[AFR][1000 genomes]
rs12310093	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17849881	0.85[EUR][1000 genomes]
rs17849882	0.85[EUR][1000 genomes]
rs28365885	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759170	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58403142	0.81[EUR][1000 genomes]
rs59965487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62636517	0.81[EUR][1000 genomes]
rs62636520	0.81[EUR][1000 genomes]
rs73306246	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 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	chr12:49659000-49663200	Transcr. at gene 5' and 3'	A549	lung
2	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
3	chr12:49659400-49664200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49659600-49662000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:49659600-49663200	Weak transcription	Fetal Brain Female	brain
6	chr12:49659600-49663400	Weak transcription	Ovary	ovary
7	chr12:49659600-49663800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:49659600-49664800	Weak transcription	Fetal Lung	lung
9	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:49659800-49662000	Transcr. at gene 5' and 3'	HMEC	breast
13	chr12:49659800-49662200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:49659800-49662200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:49659800-49662200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:49659800-49662400	Weak transcription	Brain Anterior Caudate	brain
17	chr12:49659800-49662600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:49659800-49662600	Weak transcription	Fetal Kidney	kidney
19	chr12:49659800-49663000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:49659800-49663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:49659800-49663600	Weak transcription	Primary B cells from cord blood	blood
22	chr12:49659800-49663600	Weak transcription	Aorta	Aorta
23	chr12:49659800-49663600	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:49659800-49663800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:49659800-49668600	Weak transcription	Right Atrium	heart
26	chr12:49660000-49662000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:49660000-49662000	Enhancers	Liver	Liver
28	chr12:49660000-49662000	Enhancers	Lung	lung
29	chr12:49660000-49662000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:49660000-49662200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:49660000-49662600	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:49660000-49663000	Enhancers	Adipose Nuclei	Adipose
33	chr12:49660000-49663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:49660200-49662000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
35	chr12:49660200-49662000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
36	chr12:49660200-49663200	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:49660200-49664000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:49660400-49662200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:49660400-49662800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:49660400-49662800	Transcr. at gene 5' and 3'	K562	blood
41	chr12:49660400-49663000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr12:49660400-49663200	Transcr. at gene 5' and 3'	NHEK	skin
43	chr12:49660400-49663600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:49660600-49662000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
45	chr12:49660600-49662400	Enhancers	Stomach Mucosa	stomach
46	chr12:49660600-49662800	Transcr. at gene 5' and 3'	NH-A	brain
47	chr12:49660600-49663000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
48	chr12:49660600-49663400	Transcr. at gene 5' and 3'	Hela-S3	cervix
49	chr12:49660600-49663600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:49660800-49662600	Enhancers	Primary T helper cells PMA-I stimulated	--

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