Variant report

Variant	rs4647352
Chromosome Location	chr9:98079389-98079390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:98079280-98079430	GM12865	blood:	n/a	n/a
2	CTCF	chr9:98079252-98079444	GM12892	blood:	n/a	n/a
3	MAX	chr9:98079149-98080224	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr9:98079226-98080357	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:98078881-98080518	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr9:98079341-98080173	GM12878	blood:	n/a	n/a
7	MAX	chr9:98079133-98080421	HepG2	liver:	n/a	n/a
8	CTCF	chr9:98079253-98079395	MCF-7	breast:	n/a	n/a
9	CTCF	chr9:98079256-98079453	GM19240	blood:	n/a	n/a
10	TAF1	chr9:98079248-98080252	K562	blood:	n/a	n/a
11	NR2F2	chr9:98078994-98079532	MCF-7	breast:	n/a	n/a
12	POLR2A	chr9:98079142-98080436	MCF-7	breast:	n/a	n/a
13	SIN3A	chr9:98079252-98080229	GM12878	blood:	n/a	chr9:98080192-98080201 chr9:98079792-98079803
14	TAF1	chr9:98079015-98080339	ECC-1	luminal epithelium:	n/a	n/a
15	E2F6	chr9:98079002-98080182	H1-hESC	embryonic stem cell:	n/a	chr9:98080030-98080037 chr9:98080151-98080166 chr9:98080030-98080037 chr9:98080157-98080172 chr9:98079221-98079233 chr9:98080155-98080166 chr9:98079277-98079287 chr9:98080155-98080165 chr9:98080156-98080164 chr9:98080155-98080164 chr9:98080069-98080078 chr9:98080030-98080037 chr9:98080156-98080167 chr9:98080156-98080163 chr9:98079931-98079939 chr9:98080152-98080166 chr9:98080156-98080163 chr9:98080156-98080164 chr9:98080156-98080163 chr9:98080026-98080038
16	MAZ	chr9:98078970-98080483	IMR90	lung:	n/a	n/a
17	POLR2A	chr9:98078965-98079572	ECC-1	luminal epithelium:	n/a	n/a
18	EP300	chr9:98079057-98080381	K562	blood:	n/a	chr9:98080010-98080026 chr9:98080069-98080078
19	POLR2A	chr9:98078852-98080512	U87	brain:	n/a	n/a
20	POLR2A	chr9:98079324-98080404	A549	lung:	n/a	n/a
21	NFYB	chr9:98079093-98079474	Hela-S3	cervix:	n/a	n/a
22	YY1	chr9:98079147-98080276	HepG2	liver:	n/a	chr9:98080066-98080080 chr9:98079303-98079314 chr9:98080006-98080020
23	POLR2A	chr9:98079080-98080375	NB4	blood:	n/a	n/a
24	CREB1	chr9:98079084-98080324	A549	lung:	n/a	chr9:98079739-98079752
25	EP300	chr9:98078932-98079571	A549	lung:	n/a	n/a
26	CTCF	chr9:98079240-98079390	SAEC	small airway:	n/a	n/a
27	EGR1	chr9:98079207-98079830	ECC-1	luminal epithelium:	n/a	chr9:98079246-98079256
28	CTCF	chr9:98079240-98079390	HMF	breast:	n/a	n/a
29	MAX	chr9:98079146-98080213	K562	blood:	n/a	n/a
30	ZNF143	chr9:98079196-98080309	Hela-S3	cervix:	n/a	chr9:98080191-98080201 chr9:98080069-98080079
31	CTCF	chr9:98079240-98079390	AG04449	skin:	n/a	n/a
32	CTCF	chr9:98079164-98079530	GM12878	blood:	n/a	n/a
33	POLR2A	chr9:98079113-98080391	GM12892	blood:	n/a	n/a
34	E2F4	chr9:98079069-98080320	Hela-S3	cervix:	n/a	chr9:98080030-98080037 chr9:98080027-98080038 chr9:98080151-98080166 chr9:98080030-98080037 chr9:98080157-98080172 chr9:98079221-98079233 chr9:98080155-98080166 chr9:98079277-98079287 chr9:98080155-98080165 chr9:98080156-98080164 chr9:98080155-98080164 chr9:98080069-98080078 chr9:98080030-98080037 chr9:98080156-98080167 chr9:98080156-98080163 chr9:98079931-98079939 chr9:98080152-98080166 chr9:98080156-98080163 chr9:98080156-98080164 chr9:98080156-98080163 chr9:98080026-98080038
35	SIN3AK20	chr9:98078983-98080525	MCF-7	breast:	n/a	n/a
36	POLR2A	chr9:98079103-98079519	H1-hESC	embryonic stem cell:	n/a	n/a
37	EGR1	chr9:98079152-98080409	HCT-116	colon:	n/a	chr9:98080069-98080079 chr9:98079246-98079256 chr9:98080089-98080098
38	POLR2A	chr9:98078951-98079522	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr9:98078752-98081164	HepG2	liver:	n/a	n/a
40	POLR2A	chr9:98079098-98080377	GM15510	blood:	n/a	n/a
41	CTCF	chr9:98079240-98079390	Hela-S3	cervix:	n/a	n/a
42	CEBPB	chr9:98079236-98079484	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:98079208-98080294	H1-neurons	neurons:	n/a	n/a
44	NFYB	chr9:98079132-98079503	K562	blood:	n/a	n/a
45	TBP	chr9:98079064-98080366	HepG2	liver:	n/a	n/a
46	MAX	chr9:98079072-98080255	K562	blood:	n/a	n/a
47	POLR2A	chr9:98078661-98080498	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr9:98078708-98080647	GM12891	blood:	n/a	n/a
49	CTCF	chr9:98079320-98079470	GM12867	blood:	n/a	n/a
50	POLR2A	chr9:98079042-98080445	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:27745463..27746171-chr9:98079163..98079950,2	Hela-S3	cervix:
2	chr9:98053145..98055941-chr9:98078860..98081367,2	MCF-7	breast:
3	chr9:98078160..98080305-chr9:98637483..98639375,2	MCF-7	breast:
4	chr12:54718630..54719580-chr9:98079060..98080316,3	Hela-S3	cervix:
5	chr17:40540218..40543029-chr9:98077707..98079432,2	MCF-7	breast:
6	chr9:98078552..98082181-chr9:98188850..98192317,4	MCF-7	breast:
7	chr6:32939613..32940373-chr9:98078926..98079769,3	Hela-S3	cervix:
8	chr9:98078123..98080907-chr9:98268002..98270715,3	K562	blood:
9	chr6:26158003..26158604-chr9:98078847..98079535,2	HCT-116	colon:
10	chr3:40498654..40499308-chr9:98079195..98080108,2	Hela-S3	cervix:
11	chr9:98078830..98081414-chr9:98266391..98270806,3	MCF-7	breast:
12	chr3:136471382..136472078-chr9:98079172..98080015,2	HCT-116	colon:
13	chr9:98078194..98081816-chr9:98277777..98279552,3	K562	blood:

Variant related genes	Relation type
FANCC	TF binding region
ENSG00000261758	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000188846	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000111481	Chromatin interaction
ENSG00000152484	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000230221	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000168610	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12683182	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12686588	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1875835	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2404458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3780566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs400727	0.86[JPT][hapmap]
rs4647354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647360	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647397	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647408	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647437	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647473	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647493	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647509	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4647516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7854840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9792415	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9792533	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98077400-98080400	Active TSS	GM12878-XiMat	blood
2	chr9:98078400-98080400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:98078400-98080600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:98078400-98080800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:98078600-98079400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr9:98078600-98080400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:98078600-98080400	Active TSS	Primary T cells from cord blood	blood
8	chr9:98078600-98080400	Active TSS	Colonic Mucosa	Colon
9	chr9:98078600-98080600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:98078600-98080600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr9:98078600-98080600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr9:98078600-98080600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:98078600-98080600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr9:98078600-98080600	Active TSS	Fetal Brain Male	brain
15	chr9:98078600-98080600	Active TSS	Fetal Kidney	kidney
16	chr9:98078600-98080600	Active TSS	Fetal Muscle Trunk	muscle
17	chr9:98078600-98080600	Active TSS	Stomach Smooth Muscle	stomach
18	chr9:98078600-98080600	Active TSS	Thymus	Thymus
19	chr9:98078800-98079400	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr9:98078800-98079400	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr9:98078800-98079400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr9:98078800-98079400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:98078800-98080200	Active TSS	HepG2	liver
24	chr9:98078800-98080400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:98078800-98080400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr9:98078800-98080400	Active TSS	Fetal Intestine Small	intestine
27	chr9:98078800-98080400	Active TSS	Placenta Amnion	Placenta Amnion
28	chr9:98078800-98080400	Active TSS	Right Ventricle	heart
29	chr9:98078800-98080600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:98078800-98080600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:98078800-98080600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:98078800-98080600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:98078800-98080600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:98078800-98080600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:98078800-98080600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:98078800-98080600	Active TSS	Brain Cingulate Gyrus	brain
37	chr9:98078800-98080600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:98078800-98080600	Active TSS	Colon Smooth Muscle	Colon
39	chr9:98078800-98080600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr9:98078800-98080600	Active TSS	Fetal Intestine Large	intestine
41	chr9:98078800-98080600	Active TSS	Placenta	Placenta
42	chr9:98078800-98080600	Active TSS	Fetal Stomach	stomach
43	chr9:98078800-98080600	Active TSS	Psoas Muscle	Psoas
44	chr9:98078800-98080600	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr9:98078800-98080600	Active TSS	Rectal Smooth Muscle	rectum
46	chr9:98078800-98080600	Active TSS	Stomach Mucosa	stomach
47	chr9:98078800-98080600	Active TSS	A549	lung
48	chr9:98078800-98080600	Active TSS	HSMMtube	muscle
49	chr9:98078800-98080600	Active TSS	NHDF-Ad	bronchial
50	chr9:98078800-98080800	Active TSS	HUES48 Cell Line	embryonic stem cell

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