Variant report

Variant	rs3857233
Chromosome Location	chr5:59818619-59818620
allele	A/G
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	chr5:59817657-59818738	GM12878	blood:	n/a	n/a
2	NFIC	chr5:59816967-59818822	GM12878	blood:	n/a	n/a
3	TBP	chr5:59816689-59818720	GM12878	blood:	n/a	n/a
4	CHD1	chr5:59817233-59818769	GM12878	blood:	n/a	n/a
5	MAZ	chr5:59816976-59818835	GM12878	blood:	n/a	n/a
6	BATF	chr5:59818271-59818769	GM12878	blood:	n/a	chr5:59818490-59818501
7	PBX3	chr5:59818214-59818879	SK-N-SH	brain:	n/a	n/a
8	EP300	chr5:59818360-59818732	SK-N-SH_RA	brain:	n/a	n/a
9	CUX1	chr5:59817884-59818771	GM12878	blood:	n/a	chr5:59818684-59818700
10	FOXM1	chr5:59817676-59818846	GM12878	blood:	n/a	n/a
11	TAF1	chr5:59818323-59818697	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:59818411-59818669	GM12878	blood:	n/a	n/a
13	JUND	chr5:59818165-59818941	SK-N-SH	brain:	n/a	chr5:59818445-59818455 chr5:59818445-59818455
14	IKZF1	chr5:59817320-59818764	GM12878	blood:	n/a	n/a
15	EBF1	chr5:59817897-59818728	GM12878	blood:	n/a	n/a
16	RCOR1	chr5:59817281-59819093	GM12878	blood:	n/a	n/a
17	EP300	chr5:59817369-59818839	GM12878	blood:	n/a	chr5:59817979-59817988 chr5:59817764-59817778 chr5:59817763-59817777
18	STAT5A	chr5:59817783-59818853	GM12878	blood:	n/a	chr5:59817982-59817989
19	BCL3	chr5:59818298-59818758	GM12878	blood:	n/a	chr5:59818521-59818529
20	EP300	chr5:59818152-59818920	SK-N-SH	brain:	n/a	n/a
21	ATF2	chr5:59817180-59818864	GM12878	blood:	n/a	n/a
22	NFATC1	chr5:59817720-59818686	GM12878	blood:	n/a	n/a
23	JUND	chr5:59818165-59818876	SK-N-SH	brain:	n/a	chr5:59818445-59818455 chr5:59818445-59818455
24	MEF2A	chr5:59817678-59818754	GM12878	blood:	n/a	chr5:59818253-59818264 chr5:59817965-59817979 chr5:59818073-59818088 chr5:59818254-59818263 chr5:59818065-59818080
25	SMC3	chr5:59817332-59818850	GM12878	blood:	n/a	n/a
26	BCLAF1	chr5:59818153-59818842	GM12878	blood:	n/a	chr5:59818521-59818529
27	STAT1	chr5:59817793-59818736	GM12878	blood:	n/a	chr5:59817982-59817989
28	TCF12	chr5:59818238-59818924	SK-N-SH	brain:	n/a	n/a
29	EP300	chr5:59818357-59818807	SK-N-SH_RA	brain:	n/a	n/a
30	MTA3	chr5:59817192-59818870	GM12878	blood:	n/a	n/a
31	CEBPB	chr5:59817727-59818871	GM12878	blood:	n/a	n/a
32	FOXM1	chr5:59816955-59818827	GM12878	blood:	n/a	n/a
33	YY1	chr5:59818394-59818781	GM12878	blood:	n/a	n/a
34	STAT5A	chr5:59817701-59818779	GM12878	blood:	n/a	chr5:59817982-59817989
35	BATF	chr5:59818329-59818755	GM12878	blood:	n/a	chr5:59818490-59818501
36	FOS	chr5:59818371-59818713	HUVEC	blood vessel:	n/a	chr5:59818445-59818455 chr5:59818445-59818455 chr5:59818571-59818582
37	FOSL2	chr5:59818218-59818845	SK-N-SH	brain:	n/a	chr5:59818445-59818455 chr5:59818445-59818455
38	NFIC	chr5:59816670-59818942	GM12878	blood:	n/a	n/a
39	POLR2A	chr5:59815833-59818828	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:59815831-59818879	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:59815917-59819247	GM12891	blood:	n/a	n/a
42	POLR2A	chr5:59818368-59818737	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr5:59818142-59818621	GM12891	blood:	n/a	n/a
44	GATA3	chr5:59818138-59819000	SK-N-SH	brain:	n/a	n/a
45	PBX3	chr5:59818365-59818633	GM12878	blood:	n/a	n/a
46	YY1	chr5:59818366-59818813	K562	blood:	n/a	n/a
47	POLR2A	chr5:59817640-59818731	GM12892	blood:	n/a	n/a
48	EP300	chr5:59817773-59818826	GM12878	blood:	n/a	chr5:59817979-59817988
49	POLR2A	chr5:59815410-59818932	GM12878	blood:	n/a	n/a
50	MEF2A	chr5:59817691-59818761	GM12878	blood:	n/a	chr5:59818253-59818264 chr5:59817965-59817979 chr5:59818073-59818088 chr5:59818254-59818263 chr5:59818065-59818080

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59801403..59803161-chr5:59818355..59820086,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE4D-1	chr5:59817878-59822213	XLOC_004839
2	lnc-AC109486.1-1	chr5:59816847-59822245	NONHSAT101638
3	lnc-AC109486.1-1	chr5:59816847-59822245	ENSG00000152931.7

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10516153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878197	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16878201	0.90[AMR][1000 genomes]
rs16878203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878228	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3846460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3857234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4133469	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58709164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60446062	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568722	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093135	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093138	0.90[AMR][1000 genomes]
rs73093141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110513	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73110526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7719584	0.83[AMR][1000 genomes]
rs7723069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7737012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59812800-59822400	Weak transcription	Brain Angular Gyrus	brain
2	chr5:59814000-59819600	Enhancers	Colon Smooth Muscle	Colon
3	chr5:59814800-59818800	Enhancers	Adipose Nuclei	Adipose
4	chr5:59815800-59820600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:59816000-59818800	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr5:59816600-59819600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:59816800-59818800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:59817000-59822000	Weak transcription	Fetal Thymus	thymus
9	chr5:59817400-59818800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:59817400-59819000	Enhancers	Osteobl	bone
11	chr5:59817400-59822000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:59817600-59818800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:59817600-59818800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:59817600-59819200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:59817800-59819400	Enhancers	NH-A	brain
16	chr5:59817800-59819600	Enhancers	Stomach Smooth Muscle	stomach
17	chr5:59817800-59820000	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:59817800-59829000	Weak transcription	Aorta	Aorta
19	chr5:59818000-59818800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:59818000-59819200	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr5:59818000-59822000	Weak transcription	Dnd41	blood
22	chr5:59818000-59822400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:59818000-59822400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:59818200-59818800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:59818200-59818800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:59818200-59818800	Enhancers	HUVEC	blood vessel
27	chr5:59818200-59819400	Enhancers	Fetal Stomach	stomach
28	chr5:59818200-59819800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr5:59818200-59819800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:59818400-59818800	Enhancers	Right Atrium	heart
31	chr5:59818400-59819000	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr5:59818400-59819600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr5:59818400-59820200	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:59818400-59821000	Weak transcription	HepG2	liver
35	chr5:59818400-59822600	Weak transcription	Brain Hippocampus Middle	brain
36	chr5:59818600-59818800	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:59818600-59818800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:59818600-59818800	Enhancers	Fetal Muscle Leg	muscle
39	chr5:59818600-59818800	Enhancers	Left Ventricle	heart
40	chr5:59818600-59819400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr5:59818600-59819400	Enhancers	Placenta	Placenta
42	chr5:59818600-59819400	Flanking Active TSS	GM12878-XiMat	blood
43	chr5:59818600-59821600	Weak transcription	Primary T cells from cord blood	blood

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