Variant report

Variant	rs59967511
Chromosome Location	chr9:6925240-6925241
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	EP300	chr9:6925107-6925291	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr9:6924999-6925585	SH-SY5Y	brain:	n/a	chr9:6925158-6925168
3	EP300	chr9:6925032-6925364	SK-N-SH_RA	brain:	n/a	n/a
4	FOXA1	chr9:6924994-6925283	HepG2	liver:	n/a	n/a
5	FOXA1	chr9:6925028-6925277	HepG2	liver:	n/a	n/a
6	MXI1	chr9:6923717-6925962	SK-N-SH	brain:	n/a	n/a
7	EP300	chr9:6923899-6925516	SK-N-SH	brain:	n/a	chr9:6924700-6924707
8	POLR2A	chr9:6924981-6925410	H1-neurons	neurons:	n/a	n/a
9	FOXA1	chr9:6925024-6925271	HepG2	liver:	n/a	n/a
10	POLR2A	chr9:6925039-6925376	H1-neurons	neurons:	n/a	n/a
11	FOXA1	chr9:6925032-6925319	HepG2	liver:	n/a	n/a
12	GATA3	chr9:6924900-6925253	SH-SY5Y	brain:	n/a	chr9:6925158-6925168
13	FOXA2	chr9:6925029-6925276	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10465096	0.87[ASN][1000 genomes]
rs10815476	0.89[ASN][1000 genomes]
rs10815477	0.89[ASN][1000 genomes]
rs10975878	0.87[ASN][1000 genomes]
rs10975879	0.87[ASN][1000 genomes]
rs10975895	0.90[ASN][1000 genomes]
rs10975896	0.91[ASN][1000 genomes]
rs11788152	0.83[EUR][1000 genomes]
rs11788187	0.83[EUR][1000 genomes]
rs11788687	0.82[EUR][1000 genomes]
rs11788849	0.83[EUR][1000 genomes]
rs11789124	0.80[EUR][1000 genomes]
rs11789248	0.83[EUR][1000 genomes]
rs11789250	0.83[EUR][1000 genomes]
rs11791950	0.86[EUR][1000 genomes]
rs11792447	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11793452	0.89[EUR][1000 genomes]
rs11794598	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11794707	0.83[EUR][1000 genomes]
rs11794732	0.83[EUR][1000 genomes]
rs11794905	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12684647	0.86[EUR][1000 genomes]
rs17511187	0.81[EUR][1000 genomes]
rs17595667	0.84[EUR][1000 genomes]
rs17595843	0.83[EUR][1000 genomes]
rs17595877	0.81[EUR][1000 genomes]
rs17595898	0.82[EUR][1000 genomes]
rs2890732	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55686117	0.81[EUR][1000 genomes]
rs55790433	0.81[EUR][1000 genomes]
rs55978538	0.81[AMR][1000 genomes]
rs56036039	0.81[EUR][1000 genomes]
rs56185621	0.83[EUR][1000 genomes]
rs56279813	0.81[EUR][1000 genomes]
rs56357252	0.82[EUR][1000 genomes]
rs57005961	0.81[EUR][1000 genomes]
rs58143962	0.82[EUR][1000 genomes]
rs58213169	0.82[EUR][1000 genomes]
rs58307562	0.81[EUR][1000 genomes]
rs58361204	0.82[EUR][1000 genomes]
rs58378352	0.83[EUR][1000 genomes]
rs58977474	0.82[EUR][1000 genomes]
rs59636651	0.82[EUR][1000 genomes]
rs59999598	0.83[EUR][1000 genomes]
rs60173310	0.81[EUR][1000 genomes]
rs61204407	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61685780	0.81[AMR][1000 genomes]
rs62533762	0.84[EUR][1000 genomes]
rs62533769	0.83[EUR][1000 genomes]
rs62533773	0.82[EUR][1000 genomes]
rs62533774	0.82[EUR][1000 genomes]
rs62533787	0.82[EUR][1000 genomes]
rs62533788	0.82[EUR][1000 genomes]
rs62533789	0.81[EUR][1000 genomes]
rs62533791	0.82[EUR][1000 genomes]
rs62533794	0.81[EUR][1000 genomes]
rs62533818	0.81[EUR][1000 genomes]
rs62533819	0.81[EUR][1000 genomes]
rs62533820	0.81[EUR][1000 genomes]
rs62533821	0.80[EUR][1000 genomes]
rs62533822	0.81[EUR][1000 genomes]
rs62533823	0.81[EUR][1000 genomes]
rs62533825	0.80[EUR][1000 genomes]
rs62533827	0.81[EUR][1000 genomes]
rs62533828	0.81[EUR][1000 genomes]
rs62533829	0.81[EUR][1000 genomes]
rs62533830	0.81[EUR][1000 genomes]
rs62533831	0.81[EUR][1000 genomes]
rs62533832	0.81[EUR][1000 genomes]
rs62533833	0.81[EUR][1000 genomes]
rs62533834	0.81[EUR][1000 genomes]
rs6477122	0.86[ASN][1000 genomes]
rs67642242	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67866005	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs68190370	0.82[EUR][1000 genomes]
rs7026899	0.86[EUR][1000 genomes]
rs7034789	0.89[EUR][1000 genomes]
rs72701484	0.82[EUR][1000 genomes]
rs73410616	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1024831	chr9:6573752-7018641	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	nsv892166	chr9:6602821-7222495	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv892181	chr9:6680477-7070962	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
8	nsv613252	chr9:6715730-7022554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1023906	chr9:6731786-7372132	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1023461	chr9:6774993-7022554	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv831500	chr9:6847952-6992535	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv831501	chr9:6868099-7058526	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv892184	chr9:6906384-6985602	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6889600-6929000	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
3	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:6894800-6931600	Weak transcription	Dnd41	blood
5	chr9:6896200-6959000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr9:6897600-6932200	Weak transcription	Small Intestine	intestine
7	chr9:6898200-6928800	Weak transcription	Ovary	ovary
8	chr9:6898200-6930800	Weak transcription	HSMMtube	muscle
9	chr9:6900600-6943000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:6901600-6944200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:6901800-6931600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:6902800-6931000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:6903000-6938600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:6906400-6933200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:6906600-6938200	Weak transcription	Adipose Nuclei	Adipose
16	chr9:6908800-6942600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:6912400-6927200	Weak transcription	Psoas Muscle	Psoas
18	chr9:6912400-6930800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr9:6912400-6931000	Weak transcription	Right Ventricle	heart
20	chr9:6912400-6931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:6912400-6932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:6912400-6932200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:6912400-6932200	Weak transcription	Spleen	Spleen
24	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
25	chr9:6912600-6925400	Weak transcription	Left Ventricle	heart
26	chr9:6912600-6926000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:6912600-6929600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:6915800-6925400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:6916000-6925800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:6916000-6932200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:6920200-6928800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:6920200-6930000	Weak transcription	HSMM	muscle
33	chr9:6920200-6930800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:6920200-6931000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:6920200-6931000	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:6920400-6931000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:6920600-6926800	Strong transcription	Primary T cells from cord blood	blood
38	chr9:6921400-6934000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:6921600-6925800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr9:6921600-6939200	Weak transcription	Fetal Lung	lung
41	chr9:6921600-6957600	Weak transcription	Thymus	Thymus
42	chr9:6921800-6925400	Weak transcription	Pancreas	Pancrea
43	chr9:6921800-6960400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:6922000-6928800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr9:6922000-6933600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:6922000-6941600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:6922200-6959000	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr9:6922600-6927000	Enhancers	Brain Hippocampus Middle	brain
49	chr9:6922600-6944800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:6922600-6981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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