Variant report

Variant	rs56952590
Chromosome Location	chr17:16249649-16249650
allele	A/C
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	chr17:16248780-16251384	HepG2	liver:	n/a	n/a
2	BCL3	chr17:16248745-16249688	A549	lung:	n/a	n/a
3	POLR2A	chr17:16248830-16249777	A549	lung:	n/a	n/a
4	POLR2A	chr17:16249632-16249976	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:16249641-16250803	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:16247451-16250670	K562	blood:	n/a	n/a
7	POLR2A	chr17:16248642-16249900	HepG2	liver:	n/a	n/a
8	POLR2A	chr17:16248692-16249776	HepG2	liver:	n/a	n/a
9	POLR2A	chr17:16249462-16249665	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16247522..16250151-chr17:16316906..16319854,2	K562	blood:

Variant related genes	Relation type
CENPV	TF binding region
ENSG00000187688	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1008579	0.89[AMR][1000 genomes]
rs11650283	0.81[ASN][1000 genomes]
rs11653585	0.92[ASN][1000 genomes]
rs16959630	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55861262	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62074191	0.94[ASN][1000 genomes]
rs62074192	0.94[ASN][1000 genomes]
rs8074246	0.94[ASN][1000 genomes]
rs9747806	0.87[ASN][1000 genomes]
rs9907261	0.90[ASN][1000 genomes]
rs9908541	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv962266	chr17:16245920-16260306	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr17:16229400-16255600	Weak transcription	Esophagus	oesophagus
4	chr17:16230400-16253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
6	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
8	chr17:16230600-16250800	Weak transcription	Brain Angular Gyrus	brain
9	chr17:16230600-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:16230600-16255200	Weak transcription	HSMMtube	muscle
12	chr17:16230800-16254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:16233200-16255400	Weak transcription	Right Atrium	heart
14	chr17:16238000-16255000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:16240200-16250400	Weak transcription	NH-A	brain
16	chr17:16240800-16254800	Weak transcription	HSMM	muscle
17	chr17:16241000-16255000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:16241400-16252400	Weak transcription	HUVEC	blood vessel
19	chr17:16242000-16255000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr17:16242200-16255200	Weak transcription	NHEK	skin
21	chr17:16242400-16250400	Weak transcription	Small Intestine	intestine
22	chr17:16242800-16255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:16243800-16250800	Strong transcription	Thymus	Thymus
24	chr17:16244600-16252600	Weak transcription	Psoas Muscle	Psoas
25	chr17:16244600-16254800	Weak transcription	Stomach Mucosa	stomach
26	chr17:16244800-16253200	Strong transcription	Fetal Intestine Small	intestine
27	chr17:16245200-16255200	Weak transcription	NHDF-Ad	bronchial
28	chr17:16245600-16251800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:16245600-16251800	Strong transcription	Fetal Thymus	thymus
30	chr17:16245600-16253000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr17:16245600-16253000	Strong transcription	Brain Germinal Matrix	brain
32	chr17:16245600-16253000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:16245600-16253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:16245600-16253200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:16245600-16253400	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr17:16245600-16253400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:16245600-16253400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:16245600-16253400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr17:16245600-16253400	Strong transcription	Fetal Intestine Large	intestine
40	chr17:16245600-16253400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr17:16245600-16253400	Strong transcription	Fetal Stomach	stomach
42	chr17:16245600-16253600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:16245600-16253600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr17:16245600-16253600	Strong transcription	A549	lung
45	chr17:16245600-16254200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:16245800-16250600	Strong transcription	Brain Anterior Caudate	brain
47	chr17:16245800-16250800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:16245800-16253200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr17:16245800-16253200	Strong transcription	Liver	Liver
50	chr17:16245800-16253600	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links