Variant report

Variant	rs59384952
Chromosome Location	chr3:145777799-145777800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:145777664-145778987	U87	brain:	n/a	n/a
2	POLR2A	chr3:145777552-145777883	U87	brain:	n/a	n/a
3	POLR2A	chr3:145777679-145778895	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:145777625-145778912	A549	lung:	n/a	n/a
5	POLR2A	chr3:145777486-145779048	U87	brain:	n/a	n/a
6	MBD4	chr3:145777760-145778073	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:145777540-145778011	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145769730..145771973-chr3:145775961..145777837,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLOD2-2	chr3:145777372-145779466	ENSG00000261051.1
2	lnc-AC107021.1-5	chr3:145773594-145781545	NONHSAT092545

No data

Variant related genes	Relation type
ENSG00000243415	TF binding region
ENSG00000232013	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12695805	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1449442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864794	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3749282	0.88[AFR][1000 genomes]
rs3792347	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58874363	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59850864	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67154251	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67325724	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67406460	0.80[ASN][1000 genomes]
rs67671074	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73010484	0.83[AFR][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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145762800-145785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:145763800-145779400	Weak transcription	A549	lung
3	chr3:145765000-145782000	Weak transcription	HUVEC	blood vessel
4	chr3:145768800-145788400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:145772800-145781800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:145773800-145783600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:145774600-145787200	Weak transcription	Esophagus	oesophagus
8	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
9	chr3:145775400-145782000	Weak transcription	Liver	Liver
10	chr3:145775400-145786600	Weak transcription	HepG2	liver
11	chr3:145776000-145778200	Strong transcription	HSMM	muscle
12	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
14	chr3:145776600-145787200	Weak transcription	HMEC	breast
15	chr3:145776800-145777800	Weak transcription	Fetal Stomach	stomach
16	chr3:145776800-145782400	Weak transcription	NH-A	brain
17	chr3:145776800-145783600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:145777000-145778200	Weak transcription	Fetal Heart	heart
19	chr3:145777000-145783600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:145777000-145783600	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:145777200-145782000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:145777600-145783600	Strong transcription	Osteobl	bone

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