Variant report

Variant	rs28669696
Chromosome Location	chr17:17592293-17592294
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17591306..17603641-chr17:17622226..17637880,43	MCF-7	breast:
2	chr17:17591325..17593317-chr17:17642372..17644789,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12449807	0.84[EUR][1000 genomes]
rs28536528	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58713387	1.00[ASN][1000 genomes]
rs73292256	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73294177	0.82[ASN][1000 genomes]
rs9303142	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9890330	1.00[ASN][1000 genomes]
rs9890929	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9891217	1.00[ASN][1000 genomes]
rs9891823	0.84[EUR][1000 genomes]
rs9897150	0.94[EUR][1000 genomes]
rs9905513	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907322	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
9	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
12	nsv543239	chr17:17580295-17599851	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv907755	chr17:17581184-17610587	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17587000-17593000	Weak transcription	Thymus	Thymus
2	chr17:17587200-17593400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:17587200-17593600	Weak transcription	Primary B cells from cord blood	blood
4	chr17:17587200-17594600	Weak transcription	Psoas Muscle	Psoas
5	chr17:17587200-17597000	Weak transcription	HSMMtube	muscle
6	chr17:17589000-17593800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr17:17589200-17593000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr17:17589200-17593800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr17:17589400-17593200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr17:17589400-17593600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr17:17589400-17593800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:17589400-17594600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:17589400-17595600	Weak transcription	Brain Substantia Nigra	brain
14	chr17:17589400-17595600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:17589600-17593800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:17589600-17593800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:17589600-17594400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:17589600-17594800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:17589600-17595000	Weak transcription	Small Intestine	intestine
20	chr17:17590000-17593800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:17590000-17594400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:17590000-17594400	Weak transcription	Brain Angular Gyrus	brain
23	chr17:17590000-17594400	Weak transcription	Brain Hippocampus Middle	brain
24	chr17:17590200-17593000	Weak transcription	Primary T cells from cord blood	blood
25	chr17:17590200-17593600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:17590200-17593800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:17590200-17593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:17590200-17594000	Weak transcription	Fetal Brain Female	brain
29	chr17:17590200-17594400	Weak transcription	K562	blood
30	chr17:17590200-17594400	Weak transcription	NHDF-Ad	bronchial
31	chr17:17590200-17594600	Weak transcription	Brain Anterior Caudate	brain
32	chr17:17590200-17594600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:17590200-17594600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:17590200-17594600	Weak transcription	HSMM	muscle
35	chr17:17590200-17595000	Weak transcription	Adipose Nuclei	Adipose
36	chr17:17590200-17597600	Weak transcription	Ovary	ovary
37	chr17:17590400-17593000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:17590400-17593000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:17590400-17594200	Weak transcription	Osteobl	bone
40	chr17:17590400-17594400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr17:17590400-17594400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:17590600-17592400	Strong transcription	Fetal Intestine Small	intestine
43	chr17:17590600-17592400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr17:17590600-17592600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr17:17590600-17593000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:17590600-17595000	Weak transcription	Colonic Mucosa	Colon
47	chr17:17590600-17597600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:17590800-17592600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr17:17590800-17592600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:17590800-17592600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links