Variant report

Variant	rs549334
Chromosome Location	chr11:65774659-65774660
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr11:65773955-65775210	ECC-1	luminal epithelium:	n/a	chr11:65774700-65774710
2	POLR2A	chr11:65774266-65774956	GM12878	blood:	n/a	n/a
3	EP300	chr11:65774066-65775159	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr11:65772806-65775648	U87	brain:	n/a	n/a
5	POLR2A	chr11:65772818-65775461	GM12892	blood:	n/a	n/a
6	POLR2A	chr11:65772265-65775038	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr11:65772838-65775713	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:65772812-65775253	U87	brain:	n/a	n/a
9	POLR2A	chr11:65773449-65774850	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:65774626-65775816	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:65774357-65775413	K562	blood:	n/a	n/a
12	TCF12	chr11:65773970-65775164	ECC-1	luminal epithelium:	n/a	chr11:65774700-65774710
13	POLR2A	chr11:65771689-65774819	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:65774601-65774992	Hela-S3	cervix:	n/a	n/a
15	NFIC	chr11:65774189-65775163	ECC-1	luminal epithelium:	n/a	n/a
16	NFIC	chr11:65774127-65775175	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr11:65774153-65775044	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr11:65773780-65775010	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr11:65774229-65775338	GM12892	blood:	n/a	n/a
20	ZBTB7A	chr11:65774295-65775003	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr11:65772768-65775067	GM12892	blood:	n/a	n/a
22	POLR2A	chr11:65773087-65775416	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:65773425-65775100	K562	blood:	n/a	n/a
24	POLR2A	chr11:65773416-65776059	GM12878	blood:	n/a	n/a
25	EP300	chr11:65773823-65775185	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr11:65773380-65775738	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr11:65774520-65774854	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr11:65772803-65776533	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr11:65773675-65775065	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:65772887-65775029	GM12891	blood:	n/a	n/a
31	POLR2A	chr11:65771558-65775410	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr11:65773588-65775086	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr11:65772751-65775688	GM12892	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65772051..65774698-chr11:65790348..65792220,2	MCF-7	breast:
2	chr11:65769812..65778104-chr11:65786537..65794453,15	K562	blood:
3	chr1:152007812..152009419-chr11:65774056..65776325,2	MCF-7	breast:
4	chr11:65762401..65764466-chr11:65772379..65774986,2	K562	blood:
5	chr11:65773040..65775229-chr11:66016141..66017720,2	K562	blood:
6	chr11:65772848..65775504-chr11:65827770..65830052,2	K562	blood:
7	chr11:65772402..65774686-chr11:65805406..65808291,2	MCF-7	breast:
8	chr11:65730326..65732410-chr11:65773010..65775990,2	MCF-7	breast:
9	chr11:65623667..65626453-chr11:65773319..65774880,2	MCF-7	breast:
10	chr11:65774068..65777028-chr11:65792820..65794659,2	MCF-7	breast:
11	chr11:65773321..65775670-chr11:65834388..65836189,2	K562	blood:
12	chr11:65774540..65776396-chr11:65801301..65804263,2	MCF-7	breast:

No data

Variant related genes	Relation type
CST6	TF binding region
ENSG00000087365	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11227377	0.87[AMR][1000 genomes]
rs1151510	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1151511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1151514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1191716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1192184	0.99[EUR][1000 genomes]
rs1204011	1.00[EUR][1000 genomes]
rs1786171	0.83[AMR][1000 genomes]
rs1786172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1786174	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs502363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506873	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs522553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540584	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs543952	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548435	0.83[EUR][1000 genomes]
rs548495	0.98[EUR][1000 genomes]
rs559161	0.85[AMR][1000 genomes]
rs586921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs590531	1.00[EUR][1000 genomes]
rs610497	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs615646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs616073	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs619701	1.00[EUR][1000 genomes]
rs622779	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs632640	0.83[EUR][1000 genomes]
rs645571	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs668210	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs677350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684546	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7933510	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65770800-65775200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:65771000-65776000	Weak transcription	Small Intestine	intestine
3	chr11:65771000-65779000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:65771000-65779000	Weak transcription	Aorta	Aorta
5	chr11:65771200-65774800	Strong transcription	Fetal Stomach	stomach
6	chr11:65771200-65775400	Weak transcription	HUVEC	blood vessel
7	chr11:65771200-65779000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:65771200-65779200	Weak transcription	Right Atrium	heart
9	chr11:65771400-65775000	Strong transcription	Fetal Intestine Small	intestine
10	chr11:65771800-65775000	Weak transcription	Fetal Brain Male	brain
11	chr11:65771800-65775400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:65772000-65775200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:65772000-65776200	Weak transcription	Esophagus	oesophagus
14	chr11:65772000-65776600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:65772200-65775800	Weak transcription	Colonic Mucosa	Colon
16	chr11:65772200-65776200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:65772200-65776400	Weak transcription	Brain Angular Gyrus	brain
18	chr11:65772200-65778800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:65772200-65779200	Weak transcription	Gastric	stomach
20	chr11:65772200-65779400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:65772200-65779400	Weak transcription	Psoas Muscle	Psoas
22	chr11:65772400-65778200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:65772600-65775800	Weak transcription	Fetal Intestine Large	intestine
24	chr11:65772600-65775800	Weak transcription	GM12878-XiMat	blood
25	chr11:65772600-65777200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr11:65772600-65778400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:65772800-65775800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr11:65772800-65779200	Weak transcription	Right Ventricle	heart
29	chr11:65773000-65776800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:65773200-65775400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:65773200-65775600	Weak transcription	Spleen	Spleen
32	chr11:65773200-65775800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:65773200-65776400	Weak transcription	Brain Substantia Nigra	brain
34	chr11:65773200-65776600	Weak transcription	Left Ventricle	heart
35	chr11:65773200-65776800	Weak transcription	NHDF-Ad	bronchial
36	chr11:65773200-65778000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:65773200-65778200	Weak transcription	NH-A	brain
38	chr11:65773200-65779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:65773200-65779200	Weak transcription	Colon Smooth Muscle	Colon
40	chr11:65773400-65775000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr11:65773400-65776000	Weak transcription	HSMMtube	muscle
42	chr11:65773400-65777600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr11:65773400-65778800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr11:65773400-65779000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:65773400-65779000	Weak transcription	Brain Hippocampus Middle	brain
46	chr11:65773400-65779000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:65773400-65779000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr11:65773400-65779400	Weak transcription	Ovary	ovary
49	chr11:65773400-65780200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:65773600-65775000	Weak transcription	Primary T cells fromperipheralblood	blood

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