Variant report

Variant	rs59245543
Chromosome Location	chr9:98674738-98674739
allele	A/G
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	E2F4	chr9:98674617-98674915	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr9:98674249-98675549	SK-N-SH	brain:	n/a	n/a
3	FOS	chr9:98674607-98675346	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr9:98674612-98675420	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr9:98674608-98674931	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr9:98674597-98675423	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ERCC6L2	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs58575546	1.00[AMR][1000 genomes]
rs59375678	1.00[AMR][1000 genomes]
rs73536562	1.00[AMR][1000 genomes]
rs73654829	1.00[AMR][1000 genomes]
rs73656538	1.00[AMR][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	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3496790	chr9:98674330-98678107	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3496791	chr9:98674330-98678107	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
3	chr9:98639400-98678000	Weak transcription	Ovary	ovary
4	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
8	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
9	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
12	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
16	chr9:98644400-98678400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr9:98644400-98685600	Weak transcription	Gastric	stomach
18	chr9:98644600-98678000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:98644800-98677400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:98645600-98684200	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:98645800-98678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
24	chr9:98646000-98680200	Weak transcription	K562	blood
25	chr9:98646600-98681800	Weak transcription	HSMMtube	muscle
26	chr9:98647600-98678000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:98647800-98677400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:98648200-98677800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:98648200-98678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:98649400-98676000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
33	chr9:98649600-98677400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:98649600-98679000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:98649800-98677800	Weak transcription	Osteobl	bone
36	chr9:98653800-98678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:98654000-98677200	Weak transcription	Primary T cells from cord blood	blood
38	chr9:98655200-98677400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr9:98655200-98677800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:98655200-98679800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:98658400-98678400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr9:98659000-98677200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:98659200-98685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:98659800-98684200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
46	chr9:98660200-98684000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:98661200-98677800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:98662400-98677800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:98662600-98678000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:98664000-98678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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