Variant report

Variant	rs295943
Chromosome Location	chr5:58886873-58886874
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	STAT3	chr5:58886832-58887426	MCF10A-Er-Src	breast:	n/a	chr5:58887276-58887287
2	EP300	chr5:58886865-58887384	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:58886770-58888662	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10037874	0.94[ASN][1000 genomes]
rs10805516	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs159194	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs159196	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs159197	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs177077	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs190936	0.93[EUR][1000 genomes]
rs294478	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs294479	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs294481	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs294482	0.85[ASW][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294483	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs294484	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs294485	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs294486	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294492	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs294494	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs294496	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294497	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294498	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs294499	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs294500	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs294502	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs295944	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295946	1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs295948	0.81[EUR][1000 genomes]
rs295950	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295951	0.93[EUR][1000 genomes]
rs295952	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs295953	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295954	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs295955	0.86[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs295956	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs295957	0.93[EUR][1000 genomes]
rs295958	0.93[EUR][1000 genomes]
rs295959	0.96[ASN][1000 genomes]
rs295960	0.93[EUR][1000 genomes]
rs295961	0.94[ASN][1000 genomes]
rs295962	0.93[EUR][1000 genomes]
rs295963	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs295964	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs295965	0.93[EUR][1000 genomes]
rs295966	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295967	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295968	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295969	0.93[EUR][1000 genomes]
rs295970	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs295971	0.93[EUR][1000 genomes]
rs295972	0.93[EUR][1000 genomes]
rs295973	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs295974	0.93[EUR][1000 genomes]
rs295975	0.90[EUR][1000 genomes]
rs295978	0.94[EUR][1000 genomes]
rs295979	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295980	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs298014	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs298016	0.93[EUR][1000 genomes]
rs298017	0.93[EUR][1000 genomes]
rs298025	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298027	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298028	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298029	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298030	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298032	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298033	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs298034	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs298038	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298039	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298040	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298043	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298044	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298045	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298046	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs298048	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298049	0.92[ASN][1000 genomes]
rs298051	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs298052	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs298053	0.93[EUR][1000 genomes]
rs37569	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs37571	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs431381	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58878800-58888200	Active TSS	Psoas Muscle	Psoas
2	chr5:58883800-58888800	Enhancers	Hela-S3	cervix
3	chr5:58883800-58894200	Weak transcription	Aorta	Aorta
4	chr5:58884000-58887800	Weak transcription	HSMMtube	muscle
5	chr5:58884200-58887000	Weak transcription	Brain Substantia Nigra	brain
6	chr5:58884200-58887200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr5:58884200-58888000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:58884200-58888000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:58884200-58892600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:58884200-58892600	Weak transcription	Osteobl	bone
11	chr5:58884200-58893800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:58884200-58894000	Weak transcription	Right Atrium	heart
13	chr5:58884200-58894200	Weak transcription	Liver	Liver
14	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:58884400-58887000	Weak transcription	Fetal Lung	lung
16	chr5:58884400-58888000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:58884400-58889400	Weak transcription	Brain Angular Gyrus	brain
18	chr5:58884600-58888000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr5:58884600-58888000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:58884600-58888000	Weak transcription	Brain Anterior Caudate	brain
21	chr5:58884600-58892200	Weak transcription	Small Intestine	intestine
22	chr5:58884600-58892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:58884600-58893800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:58884800-58887200	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:58884800-58887800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:58884800-58888000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:58885000-58887800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:58885000-58887800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:58885000-58892200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:58885000-58894200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:58885200-58887800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:58885200-58892400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:58885200-58892800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:58885400-58887000	Weak transcription	HSMM	muscle
35	chr5:58885400-58887800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:58885400-58892200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:58885400-58892600	Weak transcription	HUVEC	blood vessel
38	chr5:58885600-58887200	Enhancers	Stomach Mucosa	stomach
39	chr5:58886000-58887000	Enhancers	NHEK	skin
40	chr5:58886000-58888400	Enhancers	Fetal Intestine Small	intestine
41	chr5:58886200-58887000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:58886200-58887000	Enhancers	Duodenum Mucosa	Duodenum
43	chr5:58886200-58887000	Enhancers	Fetal Intestine Large	intestine
44	chr5:58886200-58888200	Enhancers	Primary B cells from peripheral blood	blood
45	chr5:58886200-58888200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr5:58886600-58887000	Active TSS	Brain Hippocampus Middle	brain
47	chr5:58886600-58887000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr5:58886600-58887000	Enhancers	GM12878-XiMat	blood
49	chr5:58886600-58887000	Enhancers	HMEC	breast
50	chr5:58886600-58887400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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