Variant report

Variant	rs4742283
Chromosome Location	chr9:7017098-7017099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10758817	0.87[EUR][1000 genomes]
rs10758818	0.87[EUR][1000 genomes]
rs10758819	0.85[EUR][1000 genomes]
rs10758821	0.81[EUR][1000 genomes]
rs10815507	0.87[EUR][1000 genomes]
rs10975971	0.92[ASN][1000 genomes]
rs10975984	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10975991	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10975992	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10975995	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12375685	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12380879	0.94[ASN][1000 genomes]
rs2031198	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2890733	0.88[ASN][1000 genomes]
rs4742281	0.91[ASN][1000 genomes]
rs7848038	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7853037	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856928	0.82[ASN][1000 genomes]
rs7858749	0.89[EUR][1000 genomes]
rs7860217	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4742283	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:7007800-7019000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr9:7008000-7018800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr9:7008000-7018800	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:7008800-7024200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:7009000-7017400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:7009000-7018000	Weak transcription	Lung	lung
11	chr9:7009000-7019000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr9:7009000-7019800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:7009000-7021600	Weak transcription	HMEC	breast
14	chr9:7009000-7026200	Weak transcription	A549	lung
15	chr9:7009000-7027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:7009000-7027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:7009000-7027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:7009000-7030400	Weak transcription	NHEK	skin
20	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
22	chr9:7009000-7055200	Weak transcription	K562	blood
23	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
24	chr9:7009000-7076600	Weak transcription	HSMM	muscle
25	chr9:7009200-7017400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:7009200-7077600	Weak transcription	Osteobl	bone
27	chr9:7009400-7019200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
29	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
30	chr9:7009600-7020400	Strong transcription	Primary B cells from cord blood	blood
31	chr9:7009800-7018000	Weak transcription	Fetal Brain Female	brain
32	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
33	chr9:7010400-7020600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:7011000-7021000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:7011200-7019600	Strong transcription	Liver	Liver
36	chr9:7011400-7018800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:7011400-7019400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr9:7011400-7020600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:7011600-7017200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:7011600-7019600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:7011600-7019800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr9:7011800-7018800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:7011800-7018800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:7012200-7018400	Strong transcription	Primary T cells from cord blood	blood
46	chr9:7012200-7018800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:7012200-7027400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:7012200-7027400	Weak transcription	Brain Anterior Caudate	brain
49	chr9:7012200-7027400	Weak transcription	Right Ventricle	heart
50	chr9:7012200-7027400	Weak transcription	Spleen	Spleen

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