Variant report

Variant	rs58925282
Chromosome Location	chr17:17390750-17390751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17379097..17381966-chr17:17388003..17390791,3	MCF-7	breast:
2	chr17:17389683..17393183-chr17:17396173..17400344,4	K562	blood:
3	chr17:17389215..17391542-chr17:17392709..17394489,2	K562	blood:
4	chr17:17389044..17391097-chr17:17393981..17396776,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction
ENSG00000141026	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs55851503	0.96[AFR][1000 genomes]
rs55888211	0.93[AFR][1000 genomes]
rs56170742	1.00[AFR][1000 genomes]
rs58205065	1.00[AFR][1000 genomes]
rs59469334	1.00[AFR][1000 genomes]
rs73978927	0.93[AFR][1000 genomes]
rs73978928	1.00[AFR][1000 genomes]
rs73978932	1.00[AFR][1000 genomes]
rs73978937	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065710	chr17:17328111-17391443	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv907730	chr17:17358004-17415217	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv827909	chr17:17358945-17394331	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv907732	chr17:17381764-17415217	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv907733	chr17:17381764-17422608	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv907734	chr17:17381764-17425858	Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv907737	chr17:17388167-17411030	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17381200-17391000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:17381200-17394200	Weak transcription	Ovary	ovary
3	chr17:17381200-17394400	Weak transcription	Aorta	Aorta
4	chr17:17381200-17395400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:17381200-17397000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:17381400-17392200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:17381400-17394400	Weak transcription	Colonic Mucosa	Colon
8	chr17:17381400-17397000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr17:17381600-17394800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr17:17381800-17391000	Weak transcription	Fetal Kidney	kidney
11	chr17:17381800-17391000	Weak transcription	NHDF-Ad	bronchial
12	chr17:17381800-17393800	Weak transcription	Fetal Lung	lung
13	chr17:17381800-17396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:17381800-17397200	Weak transcription	NH-A	brain
15	chr17:17382000-17390800	Weak transcription	Brain Substantia Nigra	brain
16	chr17:17382000-17391000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:17382000-17391000	Weak transcription	Placenta	Placenta
18	chr17:17382000-17391000	Weak transcription	Osteobl	bone
19	chr17:17382400-17396400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:17382600-17390800	Weak transcription	NHLF	lung
21	chr17:17382600-17397800	Weak transcription	Stomach Mucosa	stomach
22	chr17:17383200-17390800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr17:17383600-17391000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr17:17384000-17398000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:17384200-17391000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr17:17384400-17391000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr17:17384400-17391000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:17384400-17392400	Weak transcription	Fetal Brain Male	brain
29	chr17:17384600-17391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:17384600-17391000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr17:17384600-17391000	Weak transcription	NHEK	skin
32	chr17:17384600-17392800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:17384600-17393600	Weak transcription	Lung	lung
34	chr17:17384600-17394400	Weak transcription	Pancreas	Pancrea
35	chr17:17384600-17396800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:17385000-17390800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr17:17385000-17391000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr17:17385000-17391000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:17385600-17390800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:17385600-17390800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr17:17385600-17392400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr17:17385800-17391000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr17:17386600-17391800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:17386600-17396400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:17386600-17397400	Strong transcription	Fetal Intestine Small	intestine
46	chr17:17386600-17397800	Strong transcription	Fetal Stomach	stomach
47	chr17:17386800-17390800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:17387000-17391000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr17:17387200-17392400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:17387600-17391800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links