Variant report

Variant	rs72996210
Chromosome Location	chr3:145884871-145884872
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	SP1	chr3:145883941-145884976	A549	lung:	n/a	n/a
2	RFX5	chr3:145884089-145884953	Hela-S3	cervix:	n/a	n/a
3	EP300	chr3:145882567-145885019	A549	lung:	n/a	chr3:145884652-145884666 chr3:145884169-145884183 chr3:145883504-145883518 chr3:145883506-145883520
4	GATA3	chr3:145883999-145885146	MCF-7	breast:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
5	CEBPB	chr3:145882861-145885527	Hela-S3	cervix:	n/a	chr3:145884293-145884304 chr3:145885330-145885341 chr3:145885330-145885341 chr3:145885328-145885341
6	JUND	chr3:145883137-145884908	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr3:145884154-145884881	Hela-S3	cervix:	n/a	chr3:145884615-145884626 chr3:145884614-145884628
8	FOS	chr3:145884291-145884939	Hela-S3	cervix:	n/a	chr3:145884470-145884481
9	BRCA1	chr3:145884019-145884965	Hela-S3	cervix:	n/a	n/a
10	GATA3	chr3:145884681-145884962	T-47D	breast:	n/a	n/a
11	CEBPB	chr3:145883991-145884877	A549	lung:	n/a	chr3:145884293-145884304
12	GABPA	chr3:145884207-145884902	A549	lung:	n/a	n/a
13	GATA2	chr3:145884134-145885044	HUVEC	blood vessel:	n/a	chr3:145884196-145884203 chr3:145884193-145884205 chr3:145884194-145884204 chr3:145884259-145884269 chr3:145884196-145884206
14	SP1	chr3:145884029-145884946	A549	lung:	n/a	n/a
15	EP300	chr3:145884102-145885019	Hela-S3	cervix:	n/a	chr3:145884652-145884666 chr3:145884169-145884183
16	RCOR1	chr3:145884089-145884899	Hela-S3	cervix:	n/a	n/a
17	FOS	chr3:145884120-145884919	MCF10A-Er-Src	breast:	n/a	chr3:145884470-145884481
18	TCF12	chr3:145884057-145884972	A549	lung:	n/a	n/a
19	STAT3	chr3:145883932-145885084	MCF10A-Er-Src	breast:	n/a	n/a
20	KAP1	chr3:145884272-145884878	HEK293	kidney:	n/a	n/a
21	STAT1	chr3:145884357-145885489	Hela-S3	cervix:	n/a	n/a
22	MAX	chr3:145884034-145884931	A549	lung:	n/a	n/a
23	FOSL2	chr3:145882755-145885023	A549	lung:	n/a	n/a
24	TCF7L2	chr3:145883965-145884939	Hela-S3	cervix:	n/a	chr3:145884350-145884360
25	SMARCC1	chr3:145883678-145884953	Hela-S3	cervix:	n/a	n/a
26	MAX	chr3:145884111-145884946	Hela-S3	cervix:	n/a	n/a
27	CHD2	chr3:145884173-145884993	Hela-S3	cervix:	n/a	n/a
28	USF2	chr3:145884275-145884942	Hela-S3	cervix:	n/a	n/a
29	STAT3	chr3:145884111-145885052	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr3:145884132-145885048	MCF10A-Er-Src	breast:	n/a	n/a
31	SMC3	chr3:145884125-145884961	Hela-S3	cervix:	n/a	n/a
32	EP300	chr3:145883831-145884895	A549	lung:	n/a	chr3:145884652-145884666 chr3:145884169-145884183
33	TCF12	chr3:145883862-145885012	A549	lung:	n/a	n/a
34	MAX	chr3:145884235-145884966	Hela-S3	cervix:	n/a	n/a
35	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
36	JUN	chr3:145884104-145885035	Hela-S3	cervix:	n/a	n/a
37	REST	chr3:145884026-145885021	A549	lung:	n/a	n/a
38	SIN3AK20	chr3:145884157-145884987	MCF-7	breast:	n/a	n/a
39	STAT3	chr3:145884237-145885083	MCF10A-Er-Src	breast:	n/a	n/a
40	MAX	chr3:145884002-145885046	A549	lung:	n/a	n/a
41	FOS	chr3:145884073-145884929	MCF10A-Er-Src	breast:	n/a	chr3:145884470-145884481

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145832179..145836696-chr3:145881447..145885871,6	MCF-7	breast:
2	chr3:145884303..145885954-chr3:145902265..145904653,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLOD2-3	chr3:145884655-145884915	NONHSAT092553

Variant related genes	Relation type
PLOD2	TF binding region

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

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

rs_ID	r²[population]
rs11916662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917774	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925421	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171307	1.00[AMR][1000 genomes]
rs1375586	0.86[EUR][1000 genomes]
rs1375589	0.86[EUR][1000 genomes]
rs1512898	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512899	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16857989	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982381	0.86[EUR][1000 genomes]
rs2055978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669397	1.00[EUR][1000 genomes]
rs55721145	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57931335	1.00[AMR][1000 genomes]
rs59713697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440412	1.00[AMR][1000 genomes]
rs6440418	0.86[EUR][1000 genomes]
rs6440420	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72989683	0.99[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72989685	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72989693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72996207	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72996212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73865335	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73865338	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7626859	0.86[EUR][1000 genomes]
rs895928	1.00[EUR][1000 genomes]
rs9869319	1.00[AMR][1000 genomes]
rs9881770	0.86[EUR][1000 genomes]
rs9881772	0.86[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	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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145879800-145885000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:145880000-145885000	Enhancers	HMEC	breast
3	chr3:145880000-145885000	Enhancers	HSMMtube	muscle
4	chr3:145880000-145885000	Enhancers	NHDF-Ad	bronchial
5	chr3:145880000-145885600	Enhancers	Fetal Intestine Small	intestine
6	chr3:145880200-145885200	Enhancers	NHLF	lung
7	chr3:145880200-145885600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:145880800-145914400	Weak transcription	Left Ventricle	heart
9	chr3:145881200-145885000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:145881200-145885000	Enhancers	NHEK	skin
11	chr3:145881600-145885000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:145881600-145885400	Flanking Active TSS	A549	lung
13	chr3:145882000-145885200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:145882000-145885600	Enhancers	HUVEC	blood vessel
15	chr3:145882200-145885000	Enhancers	Fetal Intestine Large	intestine
16	chr3:145882600-145885200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr3:145882800-145885200	Enhancers	Stomach Mucosa	stomach
18	chr3:145883000-145885000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:145883000-145885200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:145883000-145885400	Enhancers	Colon Smooth Muscle	Colon
21	chr3:145883000-145885400	Enhancers	HSMM	muscle
22	chr3:145883000-145913000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:145883200-145885200	Weak transcription	Fetal Kidney	kidney
24	chr3:145883200-145885400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:145883400-145885000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:145883600-145885000	Enhancers	Adipose Nuclei	Adipose
27	chr3:145883800-145885000	Enhancers	NH-A	brain
28	chr3:145883800-145890000	Weak transcription	Fetal Heart	heart
29	chr3:145884000-145885400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:145884000-145886200	Enhancers	Osteobl	bone
31	chr3:145884000-145903400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:145884400-145885000	Enhancers	Aorta	Aorta
33	chr3:145884400-145885000	Enhancers	Pancreas	Pancrea
34	chr3:145884400-145885000	Enhancers	Small Intestine	intestine
35	chr3:145884400-145885000	Flanking Active TSS	Hela-S3	cervix
36	chr3:145884400-145885600	Enhancers	Ovary	ovary
37	chr3:145884800-145885000	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr3:145884800-145885000	Enhancers	Psoas Muscle	Psoas
39	chr3:145884800-145885600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:145884800-145885800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:145884800-145910800	Weak transcription	Liver	Liver

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