Variant report

Variant	rs35479343
Chromosome Location	chr3:145881889-145881890
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	MYC	chr3:145881334-145882050	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr3:145880956-145882397	A549	lung:	n/a	n/a
3	USF2	chr3:145881448-145882318	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:145881250-145882039	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr3:145881119-145882508	A549	lung:	n/a	n/a
6	SP1	chr3:145881068-145882299	A549	lung:	n/a	n/a
7	BCL3	chr3:145881165-145882063	A549	lung:	n/a	n/a
8	NFIC	chr3:145881364-145881898	SK-N-SH	brain:	n/a	n/a
9	EP300	chr3:145881113-145882339	A549	lung:	n/a	chr3:145881844-145881851 chr3:145882127-145882141 chr3:145881575-145881589
10	RFX5	chr3:145881351-145882337	Hela-S3	cervix:	n/a	chr3:145882150-145882164
11	POLR2A	chr3:145881143-145882012	HUVEC	blood vessel:	n/a	n/a
12	EP300	chr3:145881357-145882570	Hela-S3	cervix:	n/a	chr3:145881844-145881851 chr3:145882127-145882141 chr3:145881575-145881589
13	CEBPB	chr3:145881322-145882425	Hela-S3	cervix:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
14	STAT3	chr3:145881333-145882239	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr3:145881287-145882151	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr3:145881245-145882195	A549	lung:	n/a	n/a
17	POLR2A	chr3:145881103-145881996	HUVEC	blood vessel:	n/a	n/a
18	GATA2	chr3:145881294-145883495	HUVEC	blood vessel:	n/a	chr3:145881493-145881503 chr3:145881849-145881859
19	ATF3	chr3:145881178-145881929	A549	lung:	n/a	n/a
20	TCF7L2	chr3:145881245-145882085	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr3:145881304-145882418	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr3:145881274-145882183	A549	lung:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
23	BRCA1	chr3:145881384-145882143	Hela-S3	cervix:	n/a	n/a
24	ELF1	chr3:145881271-145881923	A549	lung:	n/a	n/a
25	SIN3AK20	chr3:145881274-145882005	A549	lung:	n/a	n/a
26	GATA3	chr3:145881396-145881931	SK-N-SH	brain:	n/a	chr3:145881493-145881503 chr3:145881849-145881859
27	FOS	chr3:145881290-145882172	MCF10A-Er-Src	breast:	n/a	n/a
28	BCL3	chr3:145881242-145882194	A549	lung:	n/a	n/a
29	MAX	chr3:145881297-145882310	Hela-S3	cervix:	n/a	chr3:145882066-145882075
30	FOS	chr3:145881244-145882631	MCF10A-Er-Src	breast:	n/a	n/a
31	CEBPB	chr3:145881352-145882257	IMR90	lung:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
32	CEBPB	chr3:145881255-145882206	MCF-7	breast:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
33	MAX	chr3:145881185-145881965	A549	lung:	n/a	n/a
34	SIX5	chr3:145881210-145882069	A549	lung:	n/a	n/a
35	MXI1	chr3:145881327-145882379	Hela-S3	cervix:	n/a	n/a
36	STAT3	chr3:145881351-145881928	MCF10A-Er-Src	breast:	n/a	n/a
37	CEBPB	chr3:145881286-145881932	MCF-7	breast:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
38	TEAD4	chr3:145881258-145881961	A549	lung:	n/a	n/a
39	JUN	chr3:145881382-145882624	Hela-S3	cervix:	n/a	n/a
40	STAT3	chr3:145881368-145882233	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr3:145881349-145881918	HCT-116	colon:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
42	TCF12	chr3:145881242-145881890	A549	lung:	n/a	n/a
43	ATF3	chr3:145881251-145881898	A549	lung:	n/a	n/a
44	CEBPB	chr3:145881178-145882375	A549	lung:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
45	EP300	chr3:145881131-145882143	A549	lung:	n/a	chr3:145881844-145881851 chr3:145882127-145882141 chr3:145881575-145881589
46	CEBPB	chr3:145881329-145882236	A549	lung:	n/a	chr3:145881574-145881585 chr3:145881594-145881605
47	GATA3	chr3:145881141-145885094	A549	lung:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145881493-145881503 chr3:145883534-145883551 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206 chr3:145881849-145881859 chr3:145883828-145883839
48	FOS	chr3:145881357-145882200	MCF10A-Er-Src	breast:	n/a	n/a
49	SP1	chr3:145881128-145882026	A549	lung:	n/a	n/a
50	JUND	chr3:145881368-145882625	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:145868830..145872262-chr3:145881585..145883218,3	MCF-7	breast:
2	chr3:145832179..145836696-chr3:145881447..145885871,6	MCF-7	breast:
3	chr3:145782122..145785411-chr3:145878106..145882365,5	MCF-7	breast:
4	chr3:145736816..145738594-chr3:145881561..145884475,2	MCF-7	breast:

Variant related genes	Relation type
PLOD2	TF binding region
ENSG00000232013	Chromatin interaction
ENSG00000243415	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13065572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13066226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13075648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13079521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13088659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13095139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34041519	0.87[AMR][1000 genomes]
rs34092280	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34201307	1.00[AFR][1000 genomes]
rs34248972	0.87[AMR][1000 genomes]
rs34298175	1.00[AMR][1000 genomes]
rs34392701	1.00[AFR][1000 genomes]
rs34589717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34695557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34901222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35017529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35020806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35080774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35520151	1.00[AFR][1000 genomes]
rs35687630	1.00[AFR][1000 genomes]
rs35880277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35969739	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62272613	1.00[AFR][1000 genomes]
rs71300372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71300373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71300374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71300377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71300378	1.00[AMR][1000 genomes]
rs71300379	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71300380	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71300381	1.00[AFR][1000 genomes]
rs71300383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71621137	1.00[AFR][1000 genomes];1.00[AMR][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	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145879400-145882000	Flanking Active TSS	HUVEC	blood vessel
2	chr3:145879400-145882000	Flanking Active TSS	Osteobl	bone
3	chr3:145879400-145882200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:145879800-145882200	Weak transcription	Psoas Muscle	Psoas
5	chr3:145879800-145882600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:145879800-145882800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:145879800-145882800	Weak transcription	Esophagus	oesophagus
8	chr3:145879800-145882800	Weak transcription	Placenta	Placenta
9	chr3:145879800-145883000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:145879800-145884400	Weak transcription	Pancreas	Pancrea
11	chr3:145879800-145885000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:145880000-145882600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:145880000-145882800	Enhancers	HSMM	muscle
14	chr3:145880000-145883000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:145880000-145883400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr3:145880000-145884400	Weak transcription	Aorta	Aorta
17	chr3:145880000-145884400	Weak transcription	Right Atrium	heart
18	chr3:145880000-145885000	Enhancers	HMEC	breast
19	chr3:145880000-145885000	Enhancers	HSMMtube	muscle
20	chr3:145880000-145885000	Enhancers	NHDF-Ad	bronchial
21	chr3:145880000-145885600	Enhancers	Fetal Intestine Small	intestine
22	chr3:145880200-145882600	Enhancers	NH-A	brain
23	chr3:145880200-145884800	Enhancers	HepG2	liver
24	chr3:145880200-145885200	Enhancers	NHLF	lung
25	chr3:145880200-145885600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:145880400-145882600	Weak transcription	Fetal Kidney	kidney
27	chr3:145880400-145883000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:145880600-145882200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:145880600-145882600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:145880600-145882600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:145880600-145882600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:145880600-145882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:145880600-145882800	Weak transcription	Gastric	stomach
34	chr3:145880600-145883400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:145880600-145883800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:145880600-145884400	Weak transcription	Fetal Lung	lung
37	chr3:145880600-145884800	Enhancers	Liver	Liver
38	chr3:145880800-145882200	Weak transcription	Fetal Intestine Large	intestine
39	chr3:145880800-145883000	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:145880800-145884400	Weak transcription	Ovary	ovary
41	chr3:145880800-145914400	Weak transcription	Left Ventricle	heart
42	chr3:145881200-145885000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:145881200-145885000	Enhancers	NHEK	skin
44	chr3:145881400-145882800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:145881400-145882800	Enhancers	Fetal Heart	heart
46	chr3:145881400-145884000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:145881600-145882000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:145881600-145882000	Flanking Active TSS	Hela-S3	cervix
49	chr3:145881600-145882200	Enhancers	Adipose Nuclei	Adipose
50	chr3:145881600-145882800	Weak transcription	Stomach Smooth Muscle	stomach

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