Variant report

Variant	rs4715428
Chromosome Location	chr6:53709740-53709741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11759220	0.81[ASN][1000 genomes]
rs12661475	0.82[ASN][1000 genomes]
rs12663216	0.83[ASN][1000 genomes]
rs2050159	0.84[EUR][1000 genomes]
rs3001004	0.81[ASN][1000 genomes]
rs3001005	0.82[ASN][1000 genomes]
rs3001006	0.82[ASN][1000 genomes]
rs3001007	0.81[ASN][1000 genomes]
rs3001008	0.81[ASN][1000 genomes]
rs3003488	0.81[ASN][1000 genomes]
rs3003490	0.81[ASN][1000 genomes]
rs3003492	0.81[ASN][1000 genomes]
rs3003494	0.81[ASN][1000 genomes]
rs35081045	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254992	0.81[ASN][1000 genomes]
rs4486000	0.82[ASN][1000 genomes]
rs4540263	0.83[ASN][1000 genomes]
rs4582388	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4618525	0.81[ASN][1000 genomes]
rs4640878	0.82[ASN][1000 genomes]
rs4715427	0.90[ASN][1000 genomes]
rs4715429	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60467893	0.80[ASN][1000 genomes]
rs6905563	0.81[ASN][1000 genomes]
rs6906326	0.82[EUR][1000 genomes]
rs6909040	0.83[ASN][1000 genomes]
rs6909094	0.83[ASN][1000 genomes]
rs6916929	0.85[EUR][1000 genomes]
rs6925391	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296720	0.81[ASN][1000 genomes]
rs9463988	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9463996	0.84[EUR][1000 genomes]
rs9463997	0.84[EUR][1000 genomes]
rs9474661	0.81[ASN][1000 genomes]
rs9474665	0.83[ASN][1000 genomes]
rs9474671	0.85[EUR][1000 genomes]
rs9474680	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:53693400-53720000	Weak transcription	Left Ventricle	heart
4	chr6:53695000-53710000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:53695000-53719800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:53697200-53718600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:53698000-53715600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:53703000-53718600	Weak transcription	Pancreas	Pancrea
10	chr6:53703200-53710400	Weak transcription	HUVEC	blood vessel
11	chr6:53703200-53720000	Weak transcription	HSMMtube	muscle
12	chr6:53703200-53720200	Weak transcription	Aorta	Aorta
13	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
14	chr6:53703400-53710200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:53703600-53710600	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:53703800-53717200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:53704400-53710600	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:53704600-53710800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:53704800-53711600	Weak transcription	Brain Germinal Matrix	brain
21	chr6:53705400-53718800	Weak transcription	NHEK	skin
22	chr6:53706000-53710400	Weak transcription	Brain Substantia Nigra	brain
23	chr6:53706000-53720200	Weak transcription	Esophagus	oesophagus
24	chr6:53706000-53722400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:53706200-53712200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:53706200-53722000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:53706400-53714400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr6:53706400-53720200	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:53706800-53710600	Enhancers	Dnd41	blood
30	chr6:53707200-53710400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:53707600-53718800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:53707800-53710800	Weak transcription	Brain Angular Gyrus	brain
33	chr6:53707800-53712800	Weak transcription	Placenta	Placenta
34	chr6:53707800-53718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:53708000-53712400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:53708400-53710200	Enhancers	Fetal Thymus	thymus
37	chr6:53708400-53711200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:53708600-53709800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:53708600-53711400	Enhancers	Thymus	Thymus
40	chr6:53708600-53712400	Weak transcription	Small Intestine	intestine
41	chr6:53708800-53710600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:53709000-53709800	Enhancers	Brain Anterior Caudate	brain
43	chr6:53709400-53709800	Strong transcription	Primary B cells from cord blood	blood
44	chr6:53709400-53710200	Strong transcription	Fetal Intestine Small	intestine
45	chr6:53709400-53718600	Weak transcription	Gastric	stomach
46	chr6:53709600-53710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:53709600-53710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:53709600-53710600	Weak transcription	Fetal Intestine Large	intestine
49	chr6:53709600-53711800	Weak transcription	HepG2	liver
50	chr6:53709600-53719800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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