Variant report

Variant	rs10975990
Chromosome Location	chr9:7026716-7026717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10758817	0.83[EUR][1000 genomes]
rs10758818	0.83[EUR][1000 genomes]
rs10758819	0.81[EUR][1000 genomes]
rs10758821	0.88[TSI][hapmap]
rs10815507	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1407862	0.88[TSI][hapmap]
rs2031198	0.85[EUR][1000 genomes]
rs2381535	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4008320	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477141	0.90[ASN][1000 genomes]
rs7027561	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7031625	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7037803	1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7041764	0.91[ASN][1000 genomes]
rs7852014	0.91[GIH][hapmap]
rs7853037	0.81[TSI][hapmap]
rs7858749	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7860217	0.83[EUR][1000 genomes]
rs818887	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1024763	chr9:7022554-7061314	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10975990	JMJD2C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:7009000-7027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:7009000-7027800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:7009000-7027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:7009000-7030400	Weak transcription	NHEK	skin
7	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
9	chr9:7009000-7055200	Weak transcription	K562	blood
10	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
11	chr9:7009000-7076600	Weak transcription	HSMM	muscle
12	chr9:7009200-7077600	Weak transcription	Osteobl	bone
13	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
14	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
15	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
16	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:7012200-7027400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:7012200-7027400	Weak transcription	Brain Anterior Caudate	brain
19	chr9:7012200-7027400	Weak transcription	Right Ventricle	heart
20	chr9:7012200-7027400	Weak transcription	Spleen	Spleen
21	chr9:7012200-7027600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
25	chr9:7012400-7028000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:7012800-7027600	Weak transcription	Esophagus	oesophagus
27	chr9:7012800-7028400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:7012800-7048800	Weak transcription	Dnd41	blood
29	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
30	chr9:7013800-7031800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:7014200-7027400	Weak transcription	Ovary	ovary
32	chr9:7014600-7048000	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:7016000-7036400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:7016200-7033200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:7016800-7027600	Weak transcription	Fetal Stomach	stomach
36	chr9:7017000-7027200	Weak transcription	Aorta	Aorta
37	chr9:7017000-7027600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:7017200-7027200	Weak transcription	Gastric	stomach
39	chr9:7017200-7028200	Weak transcription	Left Ventricle	heart
40	chr9:7017200-7028400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:7017200-7028800	Weak transcription	Fetal Muscle Leg	muscle
42	chr9:7017400-7027400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr9:7017800-7027600	Weak transcription	Thymus	Thymus
44	chr9:7017800-7075000	Weak transcription	HepG2	liver
45	chr9:7018000-7027400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:7018200-7027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:7018200-7027400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:7018200-7033200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:7018400-7027400	Weak transcription	Brain Hippocampus Middle	brain
50	chr9:7018400-7027600	Weak transcription	Fetal Intestine Large	intestine

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