Variant report

Variant	rs1093706
Chromosome Location	chr9:7009156-7009157
allele	A/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	KAP1	chr9:7009073-7009491	K562	blood:	n/a	n/a
2	SETDB1	chr9:7009039-7009381	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1093708	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1093709	0.81[EUR][1000 genomes]
rs10975958	0.83[EUR][1000 genomes]
rs10975979	0.87[JPT][hapmap]
rs10975982	0.86[JPT][hapmap]
rs10976003	0.86[JPT][hapmap]
rs10976004	0.87[JPT][hapmap]
rs10976011	0.86[JPT][hapmap]
rs1323402	0.80[JPT][hapmap]
rs16925141	0.86[JPT][hapmap]
rs1814048	1.00[JPT][hapmap]
rs2297963	0.87[JPT][hapmap]
rs2792240	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2792241	1.00[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2792242	0.92[JPT][hapmap]
rs2821446	0.93[CEU][hapmap]
rs2890734	0.86[JPT][hapmap]
rs3931591	0.83[EUR][1000 genomes]
rs752644	0.87[JPT][hapmap]
rs752645	0.87[JPT][hapmap]
rs752646	0.86[JPT][hapmap]
rs754494	0.87[JPT][hapmap]
rs8181057	0.86[JPT][hapmap]
rs8181075	0.85[JPT][hapmap]
rs818878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs818881	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs818889	0.86[JPT][hapmap]
rs818890	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs818891	0.93[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs818893	0.93[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs818894	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs818897	1.00[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs912206	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
10	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
11	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
12	nsv892185	chr9:6929053-7070962	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1021234	chr9:6933222-7015397	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv870178	chr9:6941584-7060029	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv892186	chr9:6942605-7075305	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv892187	chr9:6974101-7035727	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv949711	chr9:6994399-7045058	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv892188	chr9:6999846-7026860	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1093706	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6972000-7013200	Weak transcription	Fetal Kidney	kidney
2	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
3	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
5	chr9:6983400-7010200	Weak transcription	Stomach Mucosa	stomach
6	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:6985600-7011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:6986800-7015600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:6998000-7010400	Weak transcription	Fetal Heart	heart
12	chr9:7003400-7012800	Weak transcription	Brain Germinal Matrix	brain
13	chr9:7003600-7010400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr9:7006400-7009800	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:7007200-7009800	Strong transcription	Fetal Intestine Large	intestine
16	chr9:7007400-7009400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:7007600-7009800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr9:7007800-7019000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr9:7008000-7009200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr9:7008000-7009200	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:7008000-7009200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:7008000-7009200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:7008000-7009200	ZNF genes & repeats	Dnd41	blood
24	chr9:7008000-7009400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:7008000-7009400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr9:7008000-7009400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:7008000-7009400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:7008000-7009400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr9:7008000-7009400	Strong transcription	Colonic Mucosa	Colon
30	chr9:7008000-7009400	Strong transcription	Left Ventricle	heart
31	chr9:7008000-7009800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:7008000-7009800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:7008000-7009800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:7008000-7009800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr9:7008000-7009800	ZNF genes & repeats	GM12878-XiMat	blood
36	chr9:7008000-7009800	Strong transcription	HepG2	liver
37	chr9:7008000-7010000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:7008000-7010800	Strong transcription	Liver	Liver
39	chr9:7008000-7014200	Strong transcription	Adipose Nuclei	Adipose
40	chr9:7008000-7018800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr9:7008000-7018800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:7008200-7009200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:7008200-7009200	ZNF genes & repeats	Placenta	Placenta
44	chr9:7008200-7009400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr9:7008200-7009400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:7008200-7009400	Strong transcription	Brain Hippocampus Middle	brain
47	chr9:7008200-7009400	Strong transcription	NHDF-Ad	bronchial
48	chr9:7008200-7009600	ZNF genes & repeats	Primary B cells from cord blood	blood
49	chr9:7008200-7009600	ZNF genes & repeats	Primary T cells from cord blood	blood
50	chr9:7008200-7009600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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