Variant report

Variant	rs12375959
Chromosome Location	chr9:6872534-6872535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10758810	1.00[ASN][1000 genomes]
rs10975859	0.82[EUR][1000 genomes]
rs10975860	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10975865	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10975866	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10975868	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10975869	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10975870	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10975887	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10975937	1.00[ASN][1000 genomes]
rs12002100	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376501	0.87[EUR][1000 genomes]
rs12376520	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12376843	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12380608	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12380722	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1417291	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34266958	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34404473	0.81[AMR][1000 genomes]
rs4439184	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4567098	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60286758	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7022642	1.00[ASN][1000 genomes]
rs7038892	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7043359	0.89[EUR][1000 genomes]
rs7045367	1.00[ASN][1000 genomes]
rs73397820	1.00[ASN][1000 genomes]
rs73397828	1.00[ASN][1000 genomes]
rs7856028	1.00[ASN][1000 genomes]
rs7867730	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	esv2752309	chr9:6670448-6908200	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
11	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
12	nsv870332	chr9:6694842-6911550	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
13	nsv1016109	chr9:6712314-6924843	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
14	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
15	nsv831499	chr9:6723287-6930933	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1018557	chr9:6723728-6891136	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	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
18	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
19	nsv524069	chr9:6837912-6880263	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	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
21	esv1801159	chr9:6865386-6901008	Weak transcription Strong transcription Enhancers Genic enhancers 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
22	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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6824400-6892000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:6835400-6893200	Weak transcription	Colonic Mucosa	Colon
3	chr9:6853000-6874000	Weak transcription	Gastric	stomach
4	chr9:6864000-6880400	Weak transcription	Aorta	Aorta
5	chr9:6864200-6877400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:6864400-6874600	Weak transcription	Spleen	Spleen
7	chr9:6864400-6880200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:6864400-6880400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:6864400-6885400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr9:6864600-6873400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:6864600-6873800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:6864600-6873800	Weak transcription	HSMMtube	muscle
13	chr9:6864600-6874600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr9:6864600-6874600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:6864600-6875200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:6864600-6887200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr9:6864600-6889600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:6865000-6877800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:6865000-6887200	Weak transcription	Fetal Intestine Large	intestine
20	chr9:6865600-6877400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:6867200-6873800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:6868400-6872800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:6868400-6880200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr9:6868400-6887000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:6868800-6875200	Weak transcription	Thymus	Thymus
26	chr9:6868800-6880400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:6869000-6877800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:6869200-6898000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:6869400-6889400	Weak transcription	Adipose Nuclei	Adipose
30	chr9:6869600-6873800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:6869600-6887000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr9:6869600-6909400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr9:6869800-6873000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:6869800-6874600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:6869800-6874600	Weak transcription	Left Ventricle	heart
36	chr9:6869800-6875800	Weak transcription	Fetal Thymus	thymus
37	chr9:6869800-6876600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:6869800-6876600	Weak transcription	Lung	lung
39	chr9:6869800-6878000	Weak transcription	Right Atrium	heart
40	chr9:6869800-6880400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:6869800-6883000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:6869800-6886800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr9:6869800-6889400	Weak transcription	Right Ventricle	heart
44	chr9:6869800-6890000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:6869800-6908000	Weak transcription	Fetal Stomach	stomach
46	chr9:6870000-6873000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr9:6870000-6873800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:6870000-6874600	Weak transcription	Primary T cells from cord blood	blood
49	chr9:6870000-6888000	Weak transcription	GM12878-XiMat	blood
50	chr9:6870400-6872800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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