Variant report

Variant	rs3095174
Chromosome Location	chr17:16254494-16254495
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16254457-16254753	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16253920..16255484-chr17:16262908..16264472,2	K562	blood:
2	chr17:16254441..16256330-chr17:16335664..16338333,2	K562	blood:
3	chr17:16254424..16256101-chr17:16267326..16269115,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CENPV-1	chr17:16253943-16255093	ENSG00000250690

No data

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

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11653585	0.88[EUR][1000 genomes]
rs12603712	0.93[EUR][1000 genomes]
rs3095166	0.92[EUR][1000 genomes]
rs3112518	0.92[EUR][1000 genomes]
rs3112520	0.90[EUR][1000 genomes]
rs3112521	0.92[EUR][1000 genomes]
rs3112522	0.90[EUR][1000 genomes]
rs3112524	0.93[EUR][1000 genomes]
rs3112525	0.93[EUR][1000 genomes]
rs3112526	0.93[EUR][1000 genomes]
rs3112527	0.93[EUR][1000 genomes]
rs62074191	0.86[EUR][1000 genomes]
rs62074192	0.81[EUR][1000 genomes]
rs714285	0.92[EUR][1000 genomes]
rs72838750	0.83[EUR][1000 genomes]
rs7477	0.84[EUR][1000 genomes]
rs8071515	0.88[EUR][1000 genomes]
rs8074246	0.87[EUR][1000 genomes]
rs917609	0.93[EUR][1000 genomes]
rs9907546	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv827903	chr17:16251979-16283760	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3095174	ZSWIM7	cis	Muscle Skeletal	GTEx
rs3095174	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs3095174	CENPV	cis	Artery Tibial	GTEx
rs3095174	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
5	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
7	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:16230600-16255200	Weak transcription	HSMMtube	muscle
9	chr17:16230800-16254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:16233200-16255400	Weak transcription	Right Atrium	heart
11	chr17:16238000-16255000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr17:16240800-16254800	Weak transcription	HSMM	muscle
13	chr17:16241000-16255000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr17:16242000-16255000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:16242200-16255200	Weak transcription	NHEK	skin
16	chr17:16242800-16255000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:16244600-16254800	Weak transcription	Stomach Mucosa	stomach
18	chr17:16245200-16255200	Weak transcription	NHDF-Ad	bronchial
19	chr17:16246400-16255200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:16246600-16254800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:16246600-16255000	Weak transcription	Fetal Kidney	kidney
22	chr17:16246600-16255200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:16246800-16255000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:16246800-16255200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:16246800-16255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:16247400-16254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr17:16247800-16255200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr17:16247800-16255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:16247800-16255200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:16248000-16254600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr17:16248000-16255200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr17:16248000-16255200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:16248000-16255400	Weak transcription	Placenta	Placenta
34	chr17:16248000-16255400	Weak transcription	Ovary	ovary
35	chr17:16249600-16255200	Weak transcription	HMEC	breast
36	chr17:16250600-16255200	Weak transcription	Brain Anterior Caudate	brain
37	chr17:16250800-16254800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr17:16251800-16255400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:16252200-16255200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr17:16252200-16255200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:16252200-16255400	Weak transcription	Small Intestine	intestine
42	chr17:16252600-16254600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:16252600-16255000	Enhancers	Fetal Thymus	thymus
44	chr17:16252600-16255200	Weak transcription	Adipose Nuclei	Adipose
45	chr17:16252800-16254800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:16253000-16254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr17:16253000-16254600	Enhancers	Fetal Brain Male	brain
48	chr17:16253000-16254800	Weak transcription	HUVEC	blood vessel
49	chr17:16253000-16255000	Weak transcription	Brain Angular Gyrus	brain
50	chr17:16253000-16255000	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links