Variant report

Variant	rs1449446
Chromosome Location	chr3:145778320-145778321
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	POLR2A	chr3:145777664-145778987	U87	brain:	n/a	n/a
2	POLR2A	chr3:145777679-145778895	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:145777625-145778912	A549	lung:	n/a	n/a
4	POLR2A	chr3:145777486-145779048	U87	brain:	n/a	n/a
5	CTCF	chr3:145778280-145778430	HCFaa	heart:	n/a	n/a

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

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

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10935601	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935602	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10935604	0.83[EUR][1000 genomes]
rs1170390	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717610	0.84[EUR][1000 genomes]
rs13087364	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088180	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375580	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1375591	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1449443	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857897	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16857919	0.82[EUR][1000 genomes]
rs1982382	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762694	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792340	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792345	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804663	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804667	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611785	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681293	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681297	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56686359	0.84[EUR][1000 genomes]
rs6771106	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6771118	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781300	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783926	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792464	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7613150	0.85[EUR][1000 genomes]
rs7642940	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9820945	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836725	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869137	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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:25 , 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	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
13	chr3:145776600-145787200	Weak transcription	HMEC	breast
14	chr3:145776800-145782400	Weak transcription	NH-A	brain
15	chr3:145776800-145783600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:145777000-145783600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:145777000-145783600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:145777200-145782000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:145777600-145783600	Strong transcription	Osteobl	bone
21	chr3:145778200-145778400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:145778200-145779000	Enhancers	Fetal Heart	heart
23	chr3:145778200-145779600	Weak transcription	HSMM	muscle
24	chr3:145778200-145782400	Weak transcription	HSMMtube	muscle
25	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach

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