Variant report

Variant	rs10975992
Chromosome Location	chr9:7028066-7028067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1057199	0.84[JPT][hapmap]
rs10758817	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs10758818	0.89[EUR][1000 genomes]
rs10758819	0.87[EUR][1000 genomes]
rs10758821	0.84[EUR][1000 genomes]
rs10815507	0.89[EUR][1000 genomes]
rs10975971	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10975984	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10975991	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10975995	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12375685	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12380879	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1407862	0.82[EUR][1000 genomes]
rs2031198	0.81[AMR][1000 genomes]
rs2890733	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3802404	0.89[JPT][hapmap]
rs4742281	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4742283	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7848038	0.91[ASN][1000 genomes]
rs7853037	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7856928	0.83[ASN][1000 genomes]
rs7858749	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs7860217	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv613257	chr9:7015330-7037370	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	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
rs10975992	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	chr9:7009000-7028400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:7009000-7030400	Weak transcription	NHEK	skin
4	chr9:7009000-7044800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:7009000-7046200	Weak transcription	Small Intestine	intestine
6	chr9:7009000-7055200	Weak transcription	K562	blood
7	chr9:7009000-7056400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:7009000-7076600	Weak transcription	HSMM	muscle
9	chr9:7009200-7077600	Weak transcription	Osteobl	bone
10	chr9:7009400-7029600	Weak transcription	Hela-S3	cervix
11	chr9:7009400-7042000	Weak transcription	NHDF-Ad	bronchial
12	chr9:7009800-7076600	Weak transcription	HSMMtube	muscle
13	chr9:7011800-7048800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:7012200-7046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:7012200-7052600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:7012200-7111200	Weak transcription	Colonic Mucosa	Colon
17	chr9:7012800-7028400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:7012800-7048800	Weak transcription	Dnd41	blood
19	chr9:7012800-7076800	Weak transcription	Pancreas	Pancrea
20	chr9:7013800-7031800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr9:7014600-7048000	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:7016000-7036400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:7016200-7033200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:7017200-7028200	Weak transcription	Left Ventricle	heart
25	chr9:7017200-7028400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:7017200-7028800	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:7017800-7075000	Weak transcription	HepG2	liver
28	chr9:7018200-7033200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:7018600-7044600	Weak transcription	GM12878-XiMat	blood
30	chr9:7018600-7049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr9:7018800-7032600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:7018800-7041600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:7018800-7047200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:7018800-7047800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:7018800-7064400	Weak transcription	Psoas Muscle	Psoas
36	chr9:7019600-7046800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr9:7020000-7052800	Weak transcription	NHLF	lung
38	chr9:7023800-7028800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr9:7024000-7029800	Strong transcription	Primary B cells from cord blood	blood
40	chr9:7025200-7028200	Strong transcription	Fetal Thymus	thymus
41	chr9:7025200-7029000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:7025200-7029200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr9:7025600-7029000	Strong transcription	Primary T cells from cord blood	blood
44	chr9:7026000-7028800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:7026000-7028800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:7026000-7034800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:7026600-7029000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:7026800-7029800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr9:7027000-7028800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr9:7027000-7029000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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