Variant report

Variant	rs9378428
Chromosome Location	chr6:5548558-5548559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10484312	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12202010	0.94[JPT][hapmap]
rs2875997	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9328313	0.85[CEU][hapmap]
rs9405847	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][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	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883420	chr6:5524393-5584422	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv5181	chr6:5536921-5581595	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
2	chr6:5511400-5568200	Weak transcription	Aorta	Aorta
3	chr6:5518600-5550000	Weak transcription	Right Ventricle	heart
4	chr6:5522800-5550400	Weak transcription	GM12878-XiMat	blood
5	chr6:5523000-5549000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:5532400-5551600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:5532800-5550400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:5533000-5550400	Weak transcription	Psoas Muscle	Psoas
9	chr6:5536000-5550000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:5536800-5553000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:5538000-5550600	Weak transcription	Lung	lung
12	chr6:5538000-5573600	Weak transcription	Left Ventricle	heart
13	chr6:5538600-5550200	Weak transcription	Fetal Stomach	stomach
14	chr6:5538800-5550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:5539000-5550000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:5540400-5550600	Weak transcription	Esophagus	oesophagus
17	chr6:5541200-5550400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:5542400-5550000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:5542600-5549000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:5542600-5549600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:5542600-5550800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:5542600-5555400	Weak transcription	Gastric	stomach
23	chr6:5542800-5551000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:5543000-5549400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:5543000-5549600	Weak transcription	Placenta	Placenta
26	chr6:5543400-5550600	Weak transcription	Thymus	Thymus
27	chr6:5543600-5549400	Weak transcription	HMEC	breast
28	chr6:5544000-5550400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:5544000-5550600	Weak transcription	Dnd41	blood
30	chr6:5544200-5550000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:5544600-5550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:5544800-5550800	Weak transcription	HepG2	liver
33	chr6:5545000-5549200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:5545200-5550000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:5545200-5556600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:5545400-5560000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:5545800-5549800	Weak transcription	Fetal Intestine Large	intestine
38	chr6:5546000-5550800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:5546200-5555800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:5546400-5548600	Strong transcription	Fetal Intestine Small	intestine
41	chr6:5546600-5550600	Weak transcription	Liver	Liver
42	chr6:5547000-5550200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:5547000-5550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:5547200-5548600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:5547400-5548600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:5547400-5550200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:5547800-5548600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:5547800-5548600	Strong transcription	Small Intestine	intestine
49	chr6:5548200-5549600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:5548200-5549800	Weak transcription	Monocytes-CD14+_RO01746	blood

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