Variant report

Variant	rs1129195
Chromosome Location	chr11:64882789-64882790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 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	chr11:64882594-64883274	HCT-116	colon:	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	chr11:64882261-64883760	K562	blood:	n/a	n/a
18	POLR2A	chr11:64882118-64885676	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:64881692-64883989	K562	blood:	n/a	n/a
20	POLR2A	chr11:64881717-64885793	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:64881712-64885709	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr11:64881830-64888134	K562	blood:	n/a	n/a
23	POLR2A	chr11:64882731-64883527	ProgFib	skin:	n/a	n/a
24	HEY1	chr11:64882526-64882796	K562	blood:	n/a	n/a
25	POLR2A	chr11:64881806-64883215	Hela-S3	cervix:	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	chr11:64882636-64882866	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr11:64881262-64886939	K562	blood:	n/a	n/a
32	POLR2A	chr11:64882235-64883467	GM12878	blood:	n/a	n/a
33	POLR2A	chr11:64882210-64885647	K562	blood:	n/a	n/a
34	POLR2A	chr11:64882223-64883570	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:64881703-64887066	GM12878	blood:	n/a	n/a
36	POLR2A	chr11:64881725-64885651	GM12878	blood:	n/a	n/a
37	POLR2A	chr11:64881989-64883276	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr11:64882486-64883132	HCT-116	colon:	n/a	n/a
39	POLR2A	chr11:64881331-64883342	HepG2	liver:	n/a	n/a
40	POLR2A	chr11:64882183-64882901	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr11:64882540-64882834	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr11:64881915-64883653	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:64876666-64887064	K562	blood:	n/a	n/a
44	POLR2A	chr11:64879095-64885699	A549	lung:	n/a	n/a
45	POLR2A	chr11:64881334-64883170	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr11:64882179-64883376	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr11:64879127-64886880	GM12891	blood:	n/a	n/a
48	POLR2A	chr11:64876945-64886917	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr11:64881677-64885698	K562	blood:	n/a	n/a
50	POLR2A	chr11:64881709-64887991	GM12892	blood:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64690573..64692350-chr11:64882127..64884352,3	K562	blood:
2	chr11:64536552..64539187-chr11:64882695..64885248,2	MCF-7	breast:
3	chr11:64779861..64784378-chr11:64881512..64885598,8	MCF-7	breast:
4	chr11:64881148..64883830-chr11:64986799..64989098,2	MCF-7	breast:
5	chr11:64778393..64787449-chr11:64877655..64886980,25	K562	blood:
6	chr11:64568159..64573413-chr11:64882450..64885409,5	K562	blood:
7	chr11:64544278..64548048-chr11:64882517..64885401,5	K562	blood:
8	chr11:64849359..64854600-chr11:64874292..64883144,16	MCF-7	breast:
9	chr11:64553028..64555577-chr11:64882403..64884702,2	MCF-7	breast:
10	chr11:64862526..64865749-chr11:64882167..64886670,6	K562	blood:
11	chr11:64642261..64647543-chr11:64882719..64886329,5	MCF-7	breast:
12	chr11:64880606..64886969-chr11:64935331..64942091,20	K562	blood:
13	chr11:64877702..64891058-chr11:64944203..64957091,32	K562	blood:
14	chr11:64882671..64884203-chr11:65082144..65083671,2	K562	blood:
15	chr11:64875868..64888016-chr11:64945810..64953962,46	MCF-7	breast:
16	chr11:64881935..64884142-chr11:65015937..65018143,2	K562	blood:
17	chr11:64684925..64687410-chr11:64879641..64882846,3	MCF-7	breast:
18	chr11:64610442..64614915-chr11:64882306..64888577,8	K562	blood:
19	chr11:64778507..64787901-chr11:64877920..64890097,31	K562	blood:
20	chr11:64772580..64786543-chr11:64875055..64887722,37	MCF-7	breast:
21	chr11:64878261..64886969-chr11:64935331..64941944,21	K562	blood:
22	chr11:64877522..64908330-chr11:64931619..64960265,171	MCF-7	breast:
23	chr11:62607346..62609197-chr11:64882535..64884835,2	MCF-7	breast:
24	chr11:64881095..64883616-chr11:64967076..64970202,3	K562	blood:
25	chr11:64880986..64883460-chr11:65027641..65030397,3	K562	blood:
26	chr11:64606648..64614730-chr11:64876453..64886748,20	MCF-7	breast:
27	chr11:64881531..64883616-chr11:64967521..64970202,2	K562	blood:
28	chr11:64764345..64766401-chr11:64882130..64883731,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254501	TF binding region
ENSG00000255173	TF binding region
ENSG00000149798	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000269290	Chromatin interaction
ENSG00000168067	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000204710	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000255200	Chromatin interaction
ENSG00000014138	Chromatin interaction
ENSG00000014216	Chromatin interaction
ENSG00000197847	Chromatin interaction
ENSG00000168062	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000249251	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000254614	Chromatin interaction
ENSG00000213465	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10791813	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227118	0.97[GIH][hapmap];0.87[TSI][hapmap]
rs1196043	0.82[CEU][hapmap]
rs1206196	0.82[CEU][hapmap]
rs1300845	0.83[CHB][hapmap]
rs1706937	0.82[CEU][hapmap]
rs2282498	0.97[GIH][hapmap];0.87[TSI][hapmap]
rs2282499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3782094	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3802936	0.85[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs488686	0.83[CHB][hapmap]
rs566221	0.83[CHB][hapmap]
rs7123226	0.83[EUR][1000 genomes]
rs7943007	0.97[GIH][hapmap];0.87[TSI][hapmap]
rs947799	0.84[CHB][hapmap]
rs9971546	0.85[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1129195	FADS3	cis	cerebellum	SCAN
rs1129195	SNORD31	cis	parietal	SCAN
rs1129195	SUV420H1	cis	parietal	SCAN
rs1129195	FADS1	cis	parietal	SCAN
rs1129195	SCGB2A2	cis	cerebellum	SCAN
rs1129195	RAB1B	cis	parietal	SCAN
rs1129195	ZNHIT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64880800-64883400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr11:64880800-64883600	Weak transcription	A549	lung
3	chr11:64881000-64883000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:64881000-64883000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:64881000-64883000	Weak transcription	Right Ventricle	heart
6	chr11:64881000-64883200	Weak transcription	Gastric	stomach
7	chr11:64881000-64883200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:64881000-64883400	Weak transcription	NHDF-Ad	bronchial
9	chr11:64881000-64883600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:64881000-64883800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:64881000-64884200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:64881000-64884200	Weak transcription	Aorta	Aorta
13	chr11:64881000-64884200	Weak transcription	Right Atrium	heart
14	chr11:64881200-64882800	Enhancers	Dnd41	blood
15	chr11:64881200-64882800	Weak transcription	NHEK	skin
16	chr11:64881200-64882800	Weak transcription	NHLF	lung
17	chr11:64881200-64883000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:64881200-64883000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr11:64881200-64883000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:64881200-64883000	Weak transcription	HSMM	muscle
21	chr11:64881200-64883200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:64881200-64883200	Weak transcription	Hela-S3	cervix
23	chr11:64881200-64883200	Weak transcription	HMEC	breast
24	chr11:64881200-64883400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:64881200-64883600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:64881200-64883600	Weak transcription	Left Ventricle	heart
27	chr11:64881200-64883600	Weak transcription	NH-A	brain
28	chr11:64881200-64883800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:64881200-64883800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:64881200-64883800	Weak transcription	Psoas Muscle	Psoas
31	chr11:64881200-64883800	Weak transcription	HUVEC	blood vessel
32	chr11:64881200-64884000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr11:64881200-64884000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:64881400-64882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:64881400-64882800	Weak transcription	Adipose Nuclei	Adipose
36	chr11:64881400-64883000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:64881400-64883000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:64881400-64883000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:64881400-64883000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:64881400-64883000	Weak transcription	Stomach Mucosa	stomach
41	chr11:64881400-64883200	Weak transcription	Primary T cells from cord blood	blood
42	chr11:64881400-64883200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:64881400-64883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:64881400-64883400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:64881400-64883400	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:64881400-64883400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:64881400-64883600	Weak transcription	Primary B cells from cord blood	blood
48	chr11:64881400-64883800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr11:64881400-64883800	Weak transcription	HSMMtube	muscle
50	chr11:64881400-64884000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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