Variant report

Variant	rs1353747
Chromosome Location	chr5:58337481-58337482
allele	G/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	MYC	chr5:58333738-58337715	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
2	MAX	chr5:58334405-58337505	NB4	blood:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
3	BCL3	chr5:58335000-58338690	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
4	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
5	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
6	EP300	chr5:58334760-58337676	A549	lung:	n/a	chr5:58336263-58336277
7	EP300	chr5:58335107-58337742	A549	lung:	n/a	chr5:58336263-58336277
8	POLR2A	chr5:58336849-58337987	PFSK-1	brain:	n/a	n/a
9	CTCF	chr5:58337340-58337490	NHEK	skin:	n/a	n/a
10	GATA3	chr5:58330035-58338800	A549	lung:	n/a	chr5:58333570-58333591 chr5:58332852-58332859 chr5:58333577-58333587 chr5:58333577-58333584 chr5:58332250-58332259 chr5:58333577-58333584 chr5:58332852-58332859 chr5:58333577-58333584 chr5:58333572-58333588 chr5:58336798-58336814 chr5:58332852-58332859
11	MAX	chr5:58333100-58339130	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
12	SIX5	chr5:58337263-58339081	A549	lung:	n/a	n/a
13	POLR2A	chr5:58337152-58337637	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58336451..58338287-chr5:58345449..58347725,2	MCF-7	breast:
2	chr5:58329365..58331017-chr5:58335790..58337572,2	MCF-7	breast:

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10940640	1.00[ASW][hapmap];0.84[TSI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1498608	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1553113	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16889126	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17719258	0.82[MEX][hapmap]
rs17777413	0.87[EUR][1000 genomes]
rs2968010	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer	23535729	GWAS catalog

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336000-58338400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:58336000-58338400	Weak transcription	Gastric	stomach
3	chr5:58336000-58338600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:58336000-58343600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:58336200-58337600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:58336200-58337600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58336200-58338200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:58336200-58338200	Weak transcription	HSMMtube	muscle
9	chr5:58336200-58338400	Weak transcription	NHLF	lung
10	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
11	chr5:58336400-58337600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr5:58336400-58337600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:58336400-58337600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:58336400-58337600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:58336400-58337600	Weak transcription	Osteobl	bone
16	chr5:58336400-58337800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:58336400-58338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:58336400-58338000	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:58336400-58338000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:58336400-58338400	Enhancers	Colon Smooth Muscle	Colon
21	chr5:58336400-58338400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:58336400-58338600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr5:58336400-58338800	Enhancers	Stomach Mucosa	stomach
24	chr5:58336600-58337600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:58336600-58337800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr5:58336600-58337800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:58336600-58337800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:58336600-58338000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:58336600-58338000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:58336600-58338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:58336600-58338200	Weak transcription	Right Atrium	heart
32	chr5:58336600-58338200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:58336600-58338400	Weak transcription	Right Ventricle	heart
34	chr5:58336600-58339000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:58336600-58339000	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:58336600-58339000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:58336600-58342000	Weak transcription	Pancreas	Pancrea
38	chr5:58336600-58348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:58336600-58351800	Weak transcription	Fetal Intestine Small	intestine
40	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:58336800-58338400	Enhancers	Primary T cells from cord blood	blood
43	chr5:58336800-58338600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr5:58336800-58338800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:58336800-58338800	Enhancers	HepG2	liver
46	chr5:58336800-58339000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr5:58337000-58337600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:58337000-58338200	Enhancers	Hela-S3	cervix
49	chr5:58337000-58338600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr5:58337000-58338800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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