Variant report

Variant	rs17357002
Chromosome Location	chr4:120444056-120444057
allele	C/T
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	GATA3	chr4:120444036-120445249	SK-N-SH	brain:	n/a	chr4:120444189-120444199
2	TCF12	chr4:120444046-120445211	SK-N-SH	brain:	n/a	n/a
3	EP300	chr4:120443914-120445316	SK-N-SH	brain:	n/a	chr4:120444767-120444776 chr4:120445056-120445070 chr4:120444112-120444126 chr4:120444380-120444394 chr4:120444596-120444610
4	POLR2A	chr4:120443964-120444081	HepG2	liver:	n/a	n/a
5	GATA3	chr4:120444023-120445262	SK-N-SH	brain:	n/a	chr4:120445250-120445260 chr4:120444189-120444199

No.	Distal block	Cell Line	Cell type
1	chr4:120442633..120445586-chr4:120448509..120450219,2	MCF-7	breast:
2	chr4:120443923..120447132-chr4:120450912..120453275,3	K562	blood:
3	chr4:120442217..120444680-chr4:120461087..120463839,2	K562	blood:
4	chr4:120437151..120439080-chr4:120441248..120444121,2	K562	blood:

Variant related genes	Relation type
PDE5A	TF binding region
ENSG00000138735	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10013852	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021469	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434031	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434032	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518332	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518333	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17007472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051276	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051278	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17355550	0.93[AMR][1000 genomes]
rs17357499	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17358475	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17359764	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17359910	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17360333	0.83[EUR][1000 genomes]
rs2389872	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389876	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389877	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389878	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2389884	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953290	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4102980	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41278071	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4146266	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833621	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58613543	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58735454	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534145	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534148	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831062	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72922580	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922588	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72922598	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8180145	0.90[ASN][1000 genomes]
rs8180147	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	esv1802153	chr4:120397829-120457682	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
3	chr4:120403400-120445800	Weak transcription	A549	lung
4	chr4:120417600-120445800	Weak transcription	NHEK	skin
5	chr4:120420200-120485400	Weak transcription	Fetal Brain Male	brain
6	chr4:120420400-120449600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:120421000-120445600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:120421200-120455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:120422000-120446400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:120422800-120446600	Weak transcription	Fetal Stomach	stomach
11	chr4:120422800-120448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:120423400-120450600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:120428000-120444800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:120430800-120447400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:120433400-120444600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr4:120434600-120474400	Weak transcription	Gastric	stomach
17	chr4:120434800-120444200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:120434800-120446000	Weak transcription	HSMMtube	muscle
19	chr4:120434800-120446200	Weak transcription	HMEC	breast
20	chr4:120434800-120446400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:120434800-120448200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:120434800-120455400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:120434800-120464800	Weak transcription	Lung	lung
24	chr4:120435000-120457800	Weak transcription	Right Ventricle	heart
25	chr4:120435000-120473200	Weak transcription	Esophagus	oesophagus
26	chr4:120435000-120487600	Weak transcription	Colonic Mucosa	Colon
27	chr4:120435200-120455800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:120435400-120448000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:120436200-120473800	Weak transcription	Fetal Brain Female	brain
30	chr4:120436600-120446000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:120436600-120452800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:120436600-120455000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:120436600-120456200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:120436600-120471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:120436800-120446600	Weak transcription	Aorta	Aorta
36	chr4:120436800-120474000	Weak transcription	Thymus	Thymus
37	chr4:120437200-120444400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr4:120437600-120450600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr4:120437600-120474200	Weak transcription	Brain Substantia Nigra	brain
40	chr4:120437800-120450400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:120437800-120479200	Weak transcription	Brain Hippocampus Middle	brain
42	chr4:120438200-120444200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:120438200-120446200	Weak transcription	Ovary	ovary
44	chr4:120438200-120484800	Weak transcription	Brain Anterior Caudate	brain
45	chr4:120439200-120445400	Weak transcription	HepG2	liver
46	chr4:120439400-120446000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:120439400-120446400	Weak transcription	Fetal Heart	heart
48	chr4:120439400-120455000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr4:120439400-120455400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr4:120439400-120455800	Weak transcription	GM12878-XiMat	blood

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