Variant report

Variant	rs34419652
Chromosome Location	chr17:16334082-16334083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16333999-16334145	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:16333943-16334603	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:16334066-16334437	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:16327763..16335480-chr17:16339357..16343915,19	MCF-7	breast:
2	chr17:16283982..16285639-chr17:16332112..16335061,2	K562	blood:
3	chr17:16325375..16336653-chr17:16340697..16345018,16	MCF-7	breast:

Variant related genes	Relation type
TRPV2	TF binding region
ENSG00000170315	Chromatin interaction
ENSG00000266651	Chromatin interaction
ENSG00000175061	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11078342	0.84[AMR][1000 genomes]
rs11078343	0.84[AMR][1000 genomes]
rs11078344	0.81[AMR][1000 genomes]
rs11653149	0.81[AMR][1000 genomes]
rs11654069	0.81[AMR][1000 genomes]
rs11867498	0.81[AMR][1000 genomes]
rs11871017	0.84[AMR][1000 genomes]
rs11871929	0.81[AMR][1000 genomes]
rs11871958	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11871963	0.81[AMR][1000 genomes]
rs12936240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12940078	0.84[AMR][1000 genomes]
rs17552310	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34166276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34192401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34572942	0.84[AMR][1000 genomes]
rs34577506	0.84[AMR][1000 genomes]
rs34793697	0.81[AMR][1000 genomes]
rs34982046	0.81[AMR][1000 genomes]
rs35034622	0.81[AMR][1000 genomes]
rs35540454	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35774281	0.81[AMR][1000 genomes]
rs36117589	0.83[AMR][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	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16320000-16341400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr17:16321000-16337400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:16323200-16335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr17:16323400-16341600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr17:16323800-16334200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:16323800-16337200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:16323800-16337400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr17:16324000-16337400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:16324200-16336000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:16324200-16337400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:16324600-16337000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr17:16325200-16341400	Weak transcription	NH-A	brain
13	chr17:16325800-16334200	Strong transcription	Primary hematopoietic stem cells	blood
14	chr17:16325800-16337200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:16327000-16336600	Weak transcription	Esophagus	oesophagus
16	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:16327200-16341600	Weak transcription	Left Ventricle	heart
19	chr17:16327200-16341600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr17:16328200-16335800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:16328400-16337000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:16328400-16337200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr17:16328600-16337400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:16328600-16337400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr17:16328600-16337400	Strong transcription	Spleen	Spleen
26	chr17:16328600-16337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr17:16328600-16338000	Strong transcription	Primary T cells from cord blood	blood
28	chr17:16329400-16341400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr17:16329400-16341400	Weak transcription	Fetal Intestine Large	intestine
30	chr17:16329400-16341600	Weak transcription	Liver	Liver
31	chr17:16329600-16341400	Weak transcription	HSMMtube	muscle
32	chr17:16330000-16341400	Weak transcription	NHDF-Ad	bronchial
33	chr17:16330000-16341600	Weak transcription	Colonic Mucosa	Colon
34	chr17:16330400-16341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:16330400-16341600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:16331200-16341600	Weak transcription	HSMM	muscle
37	chr17:16331600-16336800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr17:16331600-16341600	Weak transcription	Right Ventricle	heart
39	chr17:16331800-16336600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:16331800-16341600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:16332000-16338800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr17:16332000-16341000	Strong transcription	NHLF	lung
43	chr17:16332000-16341200	Weak transcription	Fetal Intestine Small	intestine
44	chr17:16332000-16341400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:16332000-16341600	Weak transcription	Colon Smooth Muscle	Colon
46	chr17:16332000-16341600	Weak transcription	Pancreas	Pancrea
47	chr17:16332200-16338000	Weak transcription	HepG2	liver
48	chr17:16332200-16341400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr17:16332400-16336600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr17:16332600-16335000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links