Variant report

Variant	rs16959800
Chromosome Location	chr17:16440557-16440558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16438778..16440938-chr17:16486028..16489124,4	MCF-7	breast:
2	chr17:16388461..16390561-chr17:16439173..16440871,2	MCF-7	breast:
3	chr17:16438879..16441791-chr17:16451623..16453677,2	MCF-7	breast:
4	chr17:16440301..16440859-chr17:16593097..16593656,2	K562	blood:
5	chr17:16439973..16440787-chr17:16487242..16487932,3	MCF-7	breast:
6	chr17:16440172..16440870-chr17:16592489..16593852,5	MCF-7	breast:
7	chr17:16439156..16440810-chr17:16832708..16834680,2	MCF-7	breast:
8	chr17:16439915..16440775-chr17:16492573..16493244,3	MCF-7	breast:
9	chr17:16437964..16442048-chr17:16550999..16555622,7	MCF-7	breast:
10	chr17:16438989..16442073-chr17:16442104..16446030,3	MCF-7	breast:
11	chr17:16438616..16440825-chr17:16443136..16445792,4	MCF-7	breast:
12	chr17:16439908..16440839-chr17:16592969..16593878,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000170160	Chromatin interaction
ENSG00000266302	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10491106	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16959797	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16959821	0.86[AMR][1000 genomes]
rs16959828	0.86[AMR][1000 genomes]
rs28414896	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57442832	0.81[AMR][1000 genomes]
rs57502248	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211050	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213263	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214188	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214679	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217433	0.98[EUR][1000 genomes]
rs7221221	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7221367	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7224723	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73982005	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8066499	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8066627	0.96[EUR][1000 genomes]
rs8077233	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9889318	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9889728	0.81[AMR][1000 genomes]
rs9892027	0.92[EUR][1000 genomes]
rs9893954	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9904252	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911849	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
9	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 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	chr17:16438400-16440600	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr17:16438400-16440600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:16438600-16440600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:16438600-16440600	Active TSS	Stomach Smooth Muscle	stomach
5	chr17:16438600-16441000	Active TSS	Thymus	Thymus
6	chr17:16439800-16440800	Flanking Active TSS	Dnd41	blood
7	chr17:16440000-16440600	ZNF genes & repeats	GM12878-XiMat	blood
8	chr17:16440000-16440600	ZNF genes & repeats	HSMM	muscle
9	chr17:16440200-16440600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:16440200-16440600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:16440200-16440600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:16440200-16440600	Enhancers	Placenta	Placenta
13	chr17:16440200-16440600	ZNF genes & repeats	A549	lung
14	chr17:16440200-16442000	Weak transcription	Right Atrium	heart
15	chr17:16440200-16444800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:16440200-16456000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:16440400-16440600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr17:16440400-16440600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr17:16440400-16440600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr17:16440400-16440600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr17:16440400-16440600	Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr17:16440400-16440600	Enhancers	Primary B cells from peripheral blood	blood
23	chr17:16440400-16440600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr17:16440400-16440600	Enhancers	Primary hematopoietic stem cells	blood
25	chr17:16440400-16440600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr17:16440400-16440600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr17:16440400-16440600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:16440400-16440600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:16440400-16440600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr17:16440400-16440600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:16440400-16440600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:16440400-16440600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:16440400-16440600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:16440400-16440600	Enhancers	Brain Angular Gyrus	brain
35	chr17:16440400-16440600	Active TSS	Brain Anterior Caudate	brain
36	chr17:16440400-16440600	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr17:16440400-16440600	Enhancers	Colon Smooth Muscle	Colon
38	chr17:16440400-16440600	Enhancers	Esophagus	oesophagus
39	chr17:16440400-16440600	Bivalent Enhancer	Fetal Brain Female	brain
40	chr17:16440400-16440600	Enhancers	Fetal Intestine Large	intestine
41	chr17:16440400-16440600	Enhancers	Fetal Intestine Small	intestine
42	chr17:16440400-16440600	Enhancers	Pancreas	Pancrea
43	chr17:16440400-16440600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr17:16440400-16440600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr17:16440400-16440600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr17:16440400-16440600	Flanking Active TSS	HepG2	liver
47	chr17:16440400-16440800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr17:16440400-16440800	Enhancers	Adipose Nuclei	Adipose
49	chr17:16440400-16440800	Enhancers	Stomach Mucosa	stomach
50	chr17:16440400-16447400	Weak transcription	Liver	Liver

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