Variant report

Variant	rs12270532
Chromosome Location	chr11:64882163-64882164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:55)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:55 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64881621-64885776	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:64882027-64883235	U87	brain:	n/a	n/a
3	POLR2A	chr11:64879949-64886482	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:64882070-64882573	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:64881694-64890247	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:64878789-64886874	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:64881996-64885883	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:64882063-64885673	IMR90	lung:	n/a	n/a
9	POLR2A	chr11:64881743-64882918	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:64878686-64885755	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:64882084-64885696	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:64877568-64887885	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:64881900-64883302	U87	brain:	n/a	n/a
14	POLR2A	chr11:64881378-64886742	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr11:64881632-64885818	GM12892	blood:	n/a	n/a
16	POLR2A	chr11:64881239-64886927	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr11:64882118-64885676	GM12891	blood:	n/a	n/a
18	POLR2A	chr11:64881692-64883989	K562	blood:	n/a	n/a
19	POLR2A	chr11:64881717-64885793	GM12892	blood:	n/a	n/a
20	POLR2A	chr11:64881712-64885709	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr11:64882094-64882572	MCF-7	breast:	n/a	n/a
22	POLR2A	chr11:64881830-64888134	K562	blood:	n/a	n/a
23	POLR2A	chr11:64881806-64883215	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr11:64882155-64882164	ProgFib	skin:	n/a	n/a
25	POLR2A	chr11:64882080-64882431	Raji	blood:	n/a	n/a
26	POLR2A	chr11:64877637-64885859	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr11:64876227-64885692	HepG2	liver:	n/a	n/a
28	POLR2A	chr11:64881297-64885944	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:64881377-64885712	HL-60	blood:	n/a	n/a
30	POLR2A	chr11:64881262-64886939	K562	blood:	n/a	n/a
31	POLR2A	chr11:64882147-64882318	Gliobla	brain:	n/a	n/a
32	MTA3	chr11:64881994-64882498	GM12878	blood:	n/a	n/a
33	POLR2A	chr11:64882091-64882480	A549	lung:	n/a	n/a
34	POLR2A	chr11:64881703-64887066	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:64881725-64885651	GM12878	blood:	n/a	n/a
36	POLR2A	chr11:64882087-64882405	HepG2	liver:	n/a	n/a
37	POLR2A	chr11:64881989-64883276	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr11:64881763-64882617	GM12892	blood:	n/a	n/a
39	POLR2A	chr11:64881331-64883342	HepG2	liver:	n/a	n/a
40	POLR2A	chr11:64881915-64883653	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:64876666-64887064	K562	blood:	n/a	n/a
42	POLR2A	chr11:64881678-64882509	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr11:64879095-64885699	A549	lung:	n/a	n/a
44	POLR2A	chr11:64881334-64883170	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr11:64879127-64886880	GM12891	blood:	n/a	n/a
46	POLR2A	chr11:64882118-64882628	MCF-7	breast:	n/a	n/a
47	POLR2A	chr11:64876945-64886917	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr11:64881677-64885698	K562	blood:	n/a	n/a
49	POLR2A	chr11:64882085-64882665	A549	lung:	n/a	n/a
50	POLR2A	chr11:64881709-64887991	GM12892	blood:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64690573..64692350-chr11:64882127..64884352,3	K562	blood:
2	chr11:64823856..64826495-chr11:64880495..64882277,2	K562	blood:
3	chr11:64880257..64882171-chr11:65269190..65271279,2	MCF-7	breast:
4	chr11:64779861..64784378-chr11:64881512..64885598,8	MCF-7	breast:
5	chr11:64881148..64883830-chr11:64986799..64989098,2	MCF-7	breast:
6	chr11:64544538..64546780-chr11:64879402..64882290,2	MCF-7	breast:
7	chr11:64778393..64787449-chr11:64877655..64886980,25	K562	blood:
8	chr11:64849359..64854600-chr11:64874292..64883144,16	MCF-7	breast:
9	chr11:64880606..64886969-chr11:64935331..64942091,20	K562	blood:
10	chr11:64877702..64891058-chr11:64944203..64957091,32	K562	blood:
11	chr11:64643787..64646984-chr11:64875593..64882466,11	MCF-7	breast:
12	chr11:64875868..64888016-chr11:64945810..64953962,46	MCF-7	breast:
13	chr11:64881935..64884142-chr11:65015937..65018143,2	K562	blood:
14	chr11:64684925..64687410-chr11:64879641..64882846,3	MCF-7	breast:
15	chr11:64849456..64854518-chr11:64877116..64882654,9	K562	blood:
16	chr11:64778507..64787901-chr11:64877920..64890097,31	K562	blood:
17	chr11:64644806..64648507-chr11:64877927..64882201,4	MCF-7	breast:
18	chr11:64772580..64786543-chr11:64875055..64887722,37	MCF-7	breast:
19	chr11:64878261..64886969-chr11:64935331..64941944,21	K562	blood:
20	chr11:64607104..64613028-chr11:64878466..64882720,9	MCF-7	breast:
21	chr11:64616247..64617841-chr11:64881202..64882719,2	MCF-7	breast:
22	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
23	chr11:64881095..64883616-chr11:64967076..64970202,3	K562	blood:
24	chr11:64880986..64883460-chr11:65027641..65030397,3	K562	blood:
25	chr11:64606648..64614730-chr11:64876453..64886748,20	MCF-7	breast:
26	chr11:64881531..64883616-chr11:64967521..64970202,2	K562	blood:
27	chr11:64764345..64766401-chr11:64882130..64883731,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255173	TF binding region
ENSG00000254501	TF binding region
ENSG00000146670	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000255200	Chromatin interaction
ENSG00000168062	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000249251	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11227112	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11539360	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546366	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12099121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12271615	0.81[YRI][hapmap]
rs12281324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12281698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12286839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12288247	0.90[YRI][hapmap]
rs12295393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276021	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs3782095	0.90[YRI][hapmap]
rs61736623	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7936473	0.89[YRI][hapmap]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv897712	chr11:64856695-64882789	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	67 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	chr11:64880800-64882200	Enhancers	Pancreas	Pancrea
2	chr11:64880800-64882400	Weak transcription	Lung	lung
3	chr11:64880800-64883400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:64880800-64883600	Weak transcription	A549	lung
5	chr11:64881000-64882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:64881000-64882400	Enhancers	Fetal Heart	heart
7	chr11:64881000-64883000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:64881000-64883000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:64881000-64883000	Weak transcription	Right Ventricle	heart
10	chr11:64881000-64883200	Weak transcription	Gastric	stomach
11	chr11:64881000-64883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:64881000-64883400	Weak transcription	NHDF-Ad	bronchial
13	chr11:64881000-64883600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:64881000-64883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:64881000-64884200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr11:64881000-64884200	Weak transcription	Aorta	Aorta
17	chr11:64881000-64884200	Weak transcription	Right Atrium	heart
18	chr11:64881200-64882200	Weak transcription	Brain Anterior Caudate	brain
19	chr11:64881200-64882200	Genic enhancers	Fetal Brain Male	brain
20	chr11:64881200-64882200	Weak transcription	Placenta	Placenta
21	chr11:64881200-64882200	Weak transcription	Ovary	ovary
22	chr11:64881200-64882400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:64881200-64882400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:64881200-64882400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:64881200-64882400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:64881200-64882400	Enhancers	Liver	Liver
27	chr11:64881200-64882400	Weak transcription	Thymus	Thymus
28	chr11:64881200-64882600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:64881200-64882600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:64881200-64882600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:64881200-64882800	Enhancers	Dnd41	blood
32	chr11:64881200-64882800	Weak transcription	NHEK	skin
33	chr11:64881200-64882800	Weak transcription	NHLF	lung
34	chr11:64881200-64883000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:64881200-64883000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:64881200-64883000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:64881200-64883000	Weak transcription	HSMM	muscle
38	chr11:64881200-64883200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:64881200-64883200	Weak transcription	Hela-S3	cervix
40	chr11:64881200-64883200	Weak transcription	HMEC	breast
41	chr11:64881200-64883400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:64881200-64883600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:64881200-64883600	Weak transcription	Left Ventricle	heart
44	chr11:64881200-64883600	Weak transcription	NH-A	brain
45	chr11:64881200-64883800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:64881200-64883800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr11:64881200-64883800	Weak transcription	Psoas Muscle	Psoas
48	chr11:64881200-64883800	Weak transcription	HUVEC	blood vessel
49	chr11:64881200-64884000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr11:64881200-64884000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links