Variant report

Variant	rs35732562
Chromosome Location	chr9:6878215-6878216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10815474	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs10975861	0.87[CEU][hapmap];0.86[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10975871	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10975883	0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11790744	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11794707	0.86[CHD][hapmap]
rs12375929	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs17511187	0.86[CHD][hapmap]
rs17511250	0.86[CHD][hapmap]
rs17595667	0.86[CHD][hapmap]
rs17595877	0.86[CHD][hapmap]
rs56225816	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57463825	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59779500	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7033444	0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs73405231	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73639387	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7867935	0.87[CEU][hapmap]
rs946926	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35732562	KDM4C	cis	cerebellum	SCAN
rs35732562	GLDC	cis	cerebellum	SCAN

Chromatin state (count:82 , 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	chr9:6864000-6880400	Weak transcription	Aorta	Aorta
4	chr9:6864400-6880200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:6864400-6880400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:6864400-6885400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr9:6864600-6887200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr9:6864600-6889600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr9:6865000-6887200	Weak transcription	Fetal Intestine Large	intestine
10	chr9:6868400-6880200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:6868400-6887000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:6868800-6880400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:6869200-6898000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:6869400-6889400	Weak transcription	Adipose Nuclei	Adipose
15	chr9:6869600-6887000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:6869600-6909400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:6869800-6880400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:6869800-6883000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:6869800-6886800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:6869800-6889400	Weak transcription	Right Ventricle	heart
21	chr9:6869800-6890000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:6869800-6908000	Weak transcription	Fetal Stomach	stomach
23	chr9:6870000-6888000	Weak transcription	GM12878-XiMat	blood
24	chr9:6871000-6880400	Weak transcription	Pancreas	Pancrea
25	chr9:6871000-6880600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:6871000-6889400	Weak transcription	Esophagus	oesophagus
27	chr9:6871000-6902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:6871200-6879600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:6871200-6881000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:6871200-6886400	Weak transcription	Fetal Intestine Small	intestine
31	chr9:6871200-6889800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:6871200-6896000	Weak transcription	NHEK	skin
33	chr9:6871400-6880200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:6871400-6881600	Weak transcription	Liver	Liver
35	chr9:6873600-6896800	Weak transcription	Stomach Mucosa	stomach
36	chr9:6874200-6880600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:6874200-6887000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:6874200-6887000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr9:6874200-6887000	Weak transcription	Fetal Brain Male	brain
40	chr9:6874200-6889600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:6874200-6893200	Weak transcription	Brain Anterior Caudate	brain
42	chr9:6874200-6902400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:6874400-6893200	Weak transcription	Brain Hippocampus Middle	brain
44	chr9:6874400-6896600	Weak transcription	Brain Substantia Nigra	brain
45	chr9:6874800-6889400	Weak transcription	Gastric	stomach
46	chr9:6875000-6887000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:6875000-6889200	Weak transcription	Ovary	ovary
48	chr9:6875000-6902600	Weak transcription	HSMM	muscle
49	chr9:6875200-6880400	Weak transcription	Spleen	Spleen
50	chr9:6875200-6883000	Weak transcription	Monocytes-CD14+_RO01746	blood

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