Variant report

Variant	rs12339305
Chromosome Location	chr9:6959635-6959636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6952608..6955450-chr9:6959103..6961194,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10975934	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975938	0.94[AMR][1000 genomes]
rs10975939	1.00[CEU][hapmap];0.94[AMR][1000 genomes]
rs12342150	1.00[CEU][hapmap]
rs12348749	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs56722061	0.82[AMR][1000 genomes]
rs59644887	0.94[AMR][1000 genomes]
rs59881354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61290480	0.94[AMR][1000 genomes]
rs61336896	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867730	1.00[CEU][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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv1018732	chr9:6951700-6979382	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6890000-6987200	Weak transcription	Aorta	Aorta
2	chr9:6893800-6981600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:6912400-6978400	Weak transcription	Esophagus	oesophagus
4	chr9:6921800-6960400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:6922600-6981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr9:6931400-6960000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:6932800-6985000	Weak transcription	Spleen	Spleen
8	chr9:6936800-6965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:6938800-6960400	Weak transcription	Adipose Nuclei	Adipose
10	chr9:6939400-6967200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:6939400-6978600	Weak transcription	Lung	lung
12	chr9:6943600-6960000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:6945000-6981000	Weak transcription	Liver	Liver
14	chr9:6945200-6960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:6945200-6982600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:6950000-6960000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr9:6953000-6982600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:6954200-6960600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:6954200-6968200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:6954200-6994800	Weak transcription	Gastric	stomach
21	chr9:6955400-6959800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:6955400-6982400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:6955400-6982600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:6955400-6984200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:6955600-6960200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:6955600-6960400	Weak transcription	Left Ventricle	heart
27	chr9:6955600-6964000	Weak transcription	Right Ventricle	heart
28	chr9:6955600-6984200	Weak transcription	Small Intestine	intestine
29	chr9:6955800-6960600	Weak transcription	K562	blood
30	chr9:6956000-6960600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:6956000-6961000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:6956000-6963600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:6956000-6968200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr9:6956000-6971400	Weak transcription	Fetal Kidney	kidney
35	chr9:6956000-6996000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:6956200-6960000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:6956600-6960400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:6956800-6961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:6957000-6962200	Enhancers	Primary hematopoietic stem cells	blood
40	chr9:6957200-6962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:6957600-6959800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:6957800-6960400	Weak transcription	Right Atrium	heart
43	chr9:6957800-6962800	Weak transcription	Fetal Stomach	stomach
44	chr9:6957800-6964600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:6958000-6960000	Weak transcription	Fetal Lung	lung
46	chr9:6958000-6960000	Weak transcription	Psoas Muscle	Psoas
47	chr9:6958000-6961600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr9:6958000-6968800	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:6958000-6982200	Weak transcription	Ovary	ovary
50	chr9:6958000-6984000	Weak transcription	Pancreas	Pancrea

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