Variant report

Variant	rs57939654
Chromosome Location	chr17:16330994-16330995
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16330968-16331039	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:16328984-16333264	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:16330304-16333235	GM12892	blood:	n/a	n/a
4	POLR2A	chr17:16329668-16331910	K562	blood:	n/a	n/a
5	POLR2A	chr17:16330871-16331086	K562	blood:	n/a	n/a
6	ZNF263	chr17:16330947-16332049	HEK293-T-REx	kidney:	n/a	chr17:16331605-16331626
7	POLR2A	chr17:16330924-16331007	GM12878	blood:	n/a	n/a
8	CTCF	chr17:16330860-16331010	HRPEpiC	eye:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:16328263..16331417-chr17:16335355..16337965,3	K562	blood:
2	chr17:16318452..16324028-chr17:16326548..16333033,12	K562	blood:
3	chr17:16282841..16285518-chr17:16329026..16332012,2	K562	blood:
4	chr17:16327763..16335480-chr17:16339357..16343915,19	MCF-7	breast:
5	chr17:16321253..16326692-chr17:16327918..16333688,7	MCF-7	breast:
6	chr17:16325375..16336653-chr17:16340697..16345018,16	MCF-7	breast:

No data

Variant related genes	Relation type
TRPV2	TF binding region
ENSG00000175061	Chromatin interaction
ENSG00000170315	Chromatin interaction
ENSG00000264739	Chromatin interaction
ENSG00000266651	Chromatin interaction
ENSG00000187688	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1006958	1.00[EUR][1000 genomes]
rs57100283	1.00[EUR][1000 genomes]
rs57540884	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57958152	1.00[EUR][1000 genomes]
rs58069228	1.00[EUR][1000 genomes]
rs58203269	1.00[EUR][1000 genomes]
rs58213352	1.00[EUR][1000 genomes]
rs58937503	1.00[EUR][1000 genomes]
rs59191673	1.00[EUR][1000 genomes]
rs59414015	1.00[EUR][1000 genomes]
rs59837344	1.00[EUR][1000 genomes]
rs60277322	1.00[EUR][1000 genomes]
rs60436356	1.00[EUR][1000 genomes]
rs61360753	1.00[EUR][1000 genomes]
rs61479315	1.00[EUR][1000 genomes]
rs61529373	1.00[EUR][1000 genomes]
rs7212903	1.00[EUR][1000 genomes]
rs7215443	1.00[AMR][1000 genomes]
rs7217230	1.00[EUR][1000 genomes]
rs7219038	1.00[EUR][1000 genomes]
rs7224408	1.00[AMR][1000 genomes]
rs7225649	1.00[EUR][1000 genomes]
rs73281934	1.00[EUR][1000 genomes]
rs73281961	1.00[EUR][1000 genomes]
rs73281967	1.00[EUR][1000 genomes]
rs73281977	1.00[EUR][1000 genomes]
rs73281979	1.00[EUR][1000 genomes]
rs73281980	1.00[EUR][1000 genomes]
rs73281981	1.00[EUR][1000 genomes]
rs73287023	1.00[EUR][1000 genomes]
rs73287032	1.00[EUR][1000 genomes]
rs73287067	1.00[EUR][1000 genomes]
rs73287076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73287082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73287088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73287090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73287414	1.00[EUR][1000 genomes]
rs73287419	1.00[EUR][1000 genomes]
rs73287423	1.00[EUR][1000 genomes]
rs73287425	1.00[EUR][1000 genomes]
rs73287426	1.00[EUR][1000 genomes]
rs73287441	1.00[EUR][1000 genomes]
rs73288903	1.00[EUR][1000 genomes]
rs73288904	1.00[EUR][1000 genomes]
rs8066726	1.00[EUR][1000 genomes]
rs8067000	1.00[EUR][1000 genomes]
rs8068254	1.00[EUR][1000 genomes]
rs8068968	1.00[AMR][1000 genomes]
rs8069679	1.00[EUR][1000 genomes]
rs8071289	1.00[EUR][1000 genomes]
rs8075170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8079037	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16319400-16331400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr17:16320000-16341400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:16320600-16331800	Weak transcription	Brain Angular Gyrus	brain
4	chr17:16321000-16337400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:16321600-16331400	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:16323200-16335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:16323400-16331600	Strong transcription	Fetal Thymus	thymus
8	chr17:16323400-16333600	Weak transcription	A549	lung
9	chr17:16323400-16341600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:16323800-16334200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:16323800-16337200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:16323800-16337400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:16324000-16337400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:16324200-16333200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:16324200-16336000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr17:16324200-16337400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:16324600-16333200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr17:16324600-16337000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr17:16325000-16333000	Strong transcription	Osteobl	bone
20	chr17:16325200-16341400	Weak transcription	NH-A	brain
21	chr17:16325800-16332600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
22	chr17:16325800-16334200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr17:16325800-16337200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr17:16327000-16336600	Weak transcription	Esophagus	oesophagus
25	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:16327200-16341400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:16327200-16341600	Weak transcription	Left Ventricle	heart
28	chr17:16327200-16341600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr17:16328200-16333000	Strong transcription	Thymus	Thymus
30	chr17:16328200-16335800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:16328400-16337000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr17:16328400-16337200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr17:16328600-16331800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:16328600-16332000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr17:16328600-16332200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr17:16328600-16332600	Strong transcription	Ovary	ovary
37	chr17:16328600-16332600	Strong transcription	GM12878-XiMat	blood
38	chr17:16328600-16332800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:16328600-16333000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr17:16328600-16333000	Strong transcription	Dnd41	blood
41	chr17:16328600-16333200	Strong transcription	Lung	lung
42	chr17:16328600-16337400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:16328600-16337400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr17:16328600-16337400	Strong transcription	Spleen	Spleen
45	chr17:16328600-16337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr17:16328600-16338000	Strong transcription	Primary T cells from cord blood	blood
47	chr17:16328800-16331200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr17:16328800-16331200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:16328800-16332000	Enhancers	Fetal Muscle Leg	muscle
50	chr17:16328800-16332600	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links