Variant report

Variant	rs59899858
Chromosome Location	chr17:17758591-17758592
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17598092..17600072-chr17:17758359..17760671,2	MCF-7	breast:
2	chr17:17753025..17757325-chr17:17758223..17762488,4	MCF-7	breast:
3	chr17:17757374..17759870-chr17:17761758..17763640,3	K562	blood:

Variant related genes	Relation type
ENSG00000175662	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3737122	1.00[AMR][1000 genomes]
rs57006959	0.84[ASN][1000 genomes]
rs57195963	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58018883	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58628558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59929025	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61225351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
5	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
6	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
7	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
8	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
9	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
10	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' 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
11	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
12	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv907758	chr17:17619859-17782404	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
14	nsv907759	chr17:17619859-17802478	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
15	nsv1059949	chr17:17632590-17803194	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
16	nsv543244	chr17:17632590-17803194	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
17	nsv907760	chr17:17649423-17782404	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
18	nsv907761	chr17:17649423-17802478	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
19	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
20	nsv907762	chr17:17668071-17802478	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking 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 miRNA target site	72 gene(s)	inside rSNPs	diseases
21	nsv907765	chr17:17682484-17802478	Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
22	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
23	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17744400-17771400	Weak transcription	Fetal Brain Male	brain
2	chr17:17745200-17770600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:17749400-17760200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr17:17750200-17760200	Genic enhancers	Fetal Intestine Small	intestine
5	chr17:17751600-17771600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:17752200-17759600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:17753400-17759600	Weak transcription	Pancreas	Pancrea
8	chr17:17753600-17760200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr17:17753800-17759600	Weak transcription	Liver	Liver
10	chr17:17754000-17763400	Weak transcription	Hela-S3	cervix
11	chr17:17754000-17772000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr17:17754200-17759600	Weak transcription	Brain Angular Gyrus	brain
13	chr17:17754200-17764200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr17:17754200-17764600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr17:17754200-17769400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr17:17754200-17771000	Weak transcription	NH-A	brain
17	chr17:17754400-17760200	Enhancers	Fetal Intestine Large	intestine
18	chr17:17754400-17763200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr17:17754400-17763200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr17:17754400-17763200	Weak transcription	Spleen	Spleen
21	chr17:17754400-17769400	Weak transcription	Fetal Brain Female	brain
22	chr17:17754600-17759600	Weak transcription	Gastric	stomach
23	chr17:17754600-17769600	Weak transcription	Thymus	Thymus
24	chr17:17754800-17758800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:17754800-17758800	Weak transcription	Right Atrium	heart
26	chr17:17754800-17759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:17754800-17759600	Weak transcription	Psoas Muscle	Psoas
28	chr17:17754800-17769400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:17755000-17763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:17755000-17765600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:17755200-17759000	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:17755200-17759600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:17755200-17763400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr17:17755200-17763400	Weak transcription	Brain Germinal Matrix	brain
35	chr17:17755400-17759400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:17755400-17761000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr17:17755400-17763200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr17:17755400-17763400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:17755600-17763400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:17755800-17758600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:17755800-17761200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:17755800-17763200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr17:17756000-17770800	Weak transcription	Primary B cells from cord blood	blood
44	chr17:17756200-17758600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:17756200-17758800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:17756200-17759200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:17756200-17759200	Enhancers	Duodenum Mucosa	Duodenum
48	chr17:17756200-17760200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:17756200-17769600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr17:17756400-17758800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links