Variant report

Variant	rs59565323
Chromosome Location	chr3:98312492-98312493
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	GATA2	chr3:98312372-98312846	K562	blood:	n/a	chr3:98312575-98312582 chr3:98312573-98312582 chr3:98312573-98312583 chr3:98312575-98312582 chr3:98312570-98312586 chr3:98312657-98312668 chr3:98312575-98312582
2	POLR2A	chr3:98311845-98312888	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr3:98312178-98312689	A549	lung:	n/a	n/a
4	TRIM28	chr3:98312373-98312922	K562	blood:	n/a	n/a
5	ZNF143	chr3:98312114-98312806	Hela-S3	cervix:	n/a	chr3:98312514-98312532 chr3:98312521-98312530
6	EGR1	chr3:98312321-98312762	GM12878	blood:	n/a	chr3:98312492-98312507 chr3:98312493-98312507 chr3:98312496-98312505 chr3:98312493-98312506 chr3:98312494-98312508 chr3:98312494-98312505 chr3:98312493-98312506 chr3:98312492-98312502 chr3:98312489-98312511 chr3:98312496-98312506 chr3:98312493-98312506 chr3:98312493-98312506 chr3:98312509-98312533
7	TAF1	chr3:98312282-98312643	SK-N-SH	brain:	n/a	n/a
8	JUND	chr3:98312431-98312652	H1-hESC	embryonic stem cell:	n/a	chr3:98312565-98312574
9	ZBTB33	chr3:98312209-98312814	HCT-116	colon:	n/a	n/a
10	ELF1	chr3:98312226-98312938	MCF-7	breast:	n/a	chr3:98312490-98312502
11	UBTF	chr3:98311845-98312925	K562	blood:	n/a	n/a
12	GATA2	chr3:98312326-98312865	K562	blood:	n/a	chr3:98312575-98312582 chr3:98312573-98312582 chr3:98312573-98312583 chr3:98312575-98312582 chr3:98312570-98312586 chr3:98312657-98312668 chr3:98312575-98312582
13	POLR2A	chr3:98312128-98312920	GM12892	blood:	n/a	n/a
14	TAF1	chr3:98311822-98313017	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr3:98311997-98312826	K562	blood:	n/a	chr3:98312493-98312503
16	CHD2	chr3:98312327-98312945	K562	blood:	n/a	n/a
17	IKZF1	chr3:98312471-98312946	GM12878	blood:	n/a	n/a
18	GATA3	chr3:98312304-98312763	T-47D	breast:	n/a	chr3:98312575-98312582 chr3:98312573-98312582 chr3:98312573-98312583 chr3:98312575-98312582 chr3:98312570-98312586 chr3:98312657-98312668 chr3:98312574-98312582 chr3:98312575-98312582
19	GATA3	chr3:98312227-98313028	SK-N-SH	brain:	n/a	chr3:98312575-98312582 chr3:98312573-98312582 chr3:98312573-98312583 chr3:98312575-98312582 chr3:98312570-98312586 chr3:98312657-98312668 chr3:98312574-98312582 chr3:98312575-98312582
20	BHLHE40	chr3:98312301-98312931	GM12878	blood:	n/a	n/a
21	YY1	chr3:98312089-98312933	SK-N-SH_RA	brain:	n/a	chr3:98312495-98312504
22	TBP	chr3:98311874-98313188	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:98311708-98312911	GM19193	blood:	n/a	n/a
24	YY1	chr3:98312260-98312875	HCT-116	colon:	n/a	chr3:98312495-98312504
25	CTCF	chr3:98312415-98312626	Spleen_OC	spleen:	n/a	chr3:98312490-98312503
26	POLR2A	chr3:98312245-98312860	GM12891	blood:	n/a	n/a
27	CTCF	chr3:98312486-98312552	Lung_OC	lung:	n/a	chr3:98312490-98312503
28	MYC	chr3:98312450-98312724	HepG2	liver:	n/a	chr3:98312493-98312503
29	MAX	chr3:98312137-98312742	A549	lung:	n/a	chr3:98312493-98312503
30	POLR2A	chr3:98312229-98312772	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr3:98312296-98312817	SK-N-SH	brain:	n/a	n/a
32	ELK4	chr3:98312449-98312958	Hela-S3	cervix:	n/a	n/a
33	CCNT2	chr3:98311854-98312917	K562	blood:	n/a	n/a
34	JUND	chr3:98312147-98312927	A549	lung:	n/a	chr3:98312565-98312574
35	POLR2A	chr3:98311973-98312945	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr3:98311880-98313081	GM18951	blood:	n/a	n/a
37	POLR2A	chr3:98312188-98313088	GM12878	blood:	n/a	n/a
38	ETS1	chr3:98312203-98312767	GM12878	blood:	n/a	chr3:98312504-98312517 chr3:98312521-98312534 chr3:98312520-98312533 chr3:98312493-98312504
39	TBP	chr3:98312307-98313056	HepG2	liver:	n/a	n/a
40	HDAC2	chr3:98312191-98312910	HepG2	liver:	n/a	chr3:98312574-98312583 chr3:98312699-98312708
41	TAF1	chr3:98312292-98312817	GM12892	blood:	n/a	n/a
42	CTBP2	chr3:98311701-98313062	H1-hESC	embryonic stem cell:	n/a	n/a
43	RCOR1	chr3:98312424-98313006	HepG2	liver:	n/a	n/a
44	EP300	chr3:98312245-98312669	SK-N-SH_RA	brain:	n/a	chr3:98312552-98312568
45	YY1	chr3:98311574-98313002	GM12878	blood:	n/a	chr3:98312495-98312504
46	GABPA	chr3:98312183-98312616	HepG2	liver:	n/a	n/a
47	TBL1XR1	chr3:98312414-98312968	K562	blood:	n/a	n/a
48	BHLHE40	chr3:98311877-98312920	HepG2	liver:	n/a	n/a
49	PML	chr3:98312369-98312830	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:98312261-98312821	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98312473-98312523	BE2_C	brain:	n/a
2	chr3:98312473-98312523	A549	lung:	n/a
3	chr3:98312473-98312523	NHBE	bronchial:	n/a
4	chr3:98312473-98312523	IMR90	lung:	fetal
5	chr3:98312473-98312523	HL-60	blood:	n/a
6	chr3:98312473-98312523	SKMC	muscle:	n/a
7	chr3:98312473-98312523	NT2-D1	testis:	n/a
8	chr3:98312473-98312523	HCM	heart:	n/a
9	chr3:98312473-98312523	Hela-S3	cervix:	n/a
10	chr3:98312473-98312523	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:98312473-98312523	HRCEpiC	kidney:	n/a
12	chr3:98312473-98312523	NH-A	brain:	n/a
13	chr3:98312473-98312523	HRE	kidney:	n/a
14	chr3:98312473-98312523	HAEpiC	amniotic membrane:	n/a
15	chr3:98312473-98312523	AG04450	lung:	fetal
16	chr3:98312473-98312523	CMK	blood:	n/a
17	chr3:98312473-98312523	HUVEC	blood vessel:	n/a
18	chr3:98312473-98312523	Jurkat	blood:	n/a
19	chr3:98312473-98312523	SK-N-SH_RA	brain:	n/a
20	chr3:98312473-98312523	HCPEpiC	choroid plexus:	n/a
21	chr3:98312473-98312523	AoSMC	blood vessel:	n/a
22	chr3:98312473-98312523	SK-N-MC	brain:	n/a
23	chr3:98312473-98312523	HMEC	breast:	n/a
24	chr3:98312473-98312523	GM12878	blood:	n/a
25	chr3:98312473-98312523	MCF10A-Er-Src	breast:	n/a
26	chr3:98312473-98312523	SK-N-SH	brain:	n/a
27	chr3:98312473-98312523	LNCaP	prostate:	n/a
28	chr3:98312473-98312523	AG09319	gingival:	n/a
29	chr3:98312473-98312523	T-47D	breast:	n/a
30	chr3:98312473-98312523	H1-hESC	embryonic stem cell:	embryo
31	chr3:98312473-98312523	HEK293	kidney:	embryo
32	chr3:98312473-98312523	HNPCEpiC	eye:	n/a
33	chr3:98312473-98312523	AG10803	skin:	n/a
34	chr3:98312473-98312523	ovcar-3	ovarian:	n/a
35	chr3:98312473-98312523	HIPEpiC	eye:	n/a
36	chr3:98312473-98312523	HCF	heart:	n/a
37	chr3:98312473-98312523	MCF-7	breast:	n/a
38	chr3:98312473-98312523	NHDF-neo	bronchial:	n/a
39	chr3:98312473-98312523	ProgFib	skin:	n/a
40	chr3:98312473-98312523	HEEpiC	esophagus:	n/a
41	chr3:98312473-98312523	RPTEC	kidney:	n/a
42	chr3:98312473-98312523	GM12891	blood:	n/a
43	chr3:98312473-98312523	HepG2	liver:	n/a
44	chr3:98312473-98312523	GM06990	blood:	n/a
45	chr3:98312473-98312523	BJ	skin:	n/a
46	chr3:98312473-98312523	AG04449	skin:	fetal
47	chr3:98312473-98312523	AG09309	skin:	n/a
48	chr3:98312473-98312523	PrEC	prostate:	n/a
49	chr3:98312473-98312523	HCT-116	colon:	n/a
50	chr3:98312473-98312523	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:98240168..98242320-chr3:98310651..98312763,2	K562	blood:
2	chr3:98303079..98305719-chr3:98311231..98314146,3	K562	blood:
3	chr3:98311356..98313726-chr3:98530079..98532585,2	MCF-7	breast:
4	chr16:68344315..68345025-chr3:98311977..98312615,2	HCT-116	colon:
5	chr3:98303079..98306972-chr3:98311108..98314146,5	K562	blood:

Variant related genes	Relation type
CPOX	TF binding region
CPOX	CpG island
ENSG00000080822	Chromatin interaction
ENSG00000248839	Chromatin interaction
ENSG00000057019	Chromatin interaction
ENSG00000080819	Chromatin interaction
ENSG00000103061	Chromatin interaction
ENSG00000132600	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs58911313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858607	1.00[AMR][1000 genomes]
rs73858722	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv997484	chr3:98284283-98371420	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1000357	chr3:98284283-98381473	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv536661	chr3:98286588-98315764	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98310000-98312800	Active TSS	K562	blood
2	chr3:98310000-98313200	Active TSS	Brain Hippocampus Middle	brain
3	chr3:98310200-98312800	Active TSS	GM12878-XiMat	blood
4	chr3:98310200-98313000	Active TSS	Brain Substantia Nigra	brain
5	chr3:98310400-98313000	Active TSS	Brain Angular Gyrus	brain
6	chr3:98310600-98313000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:98310600-98313200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:98310800-98313200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:98310800-98313200	Active TSS	Right Atrium	heart
10	chr3:98311000-98312800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:98311000-98313000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:98311000-98313200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:98311000-98313200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:98311000-98313200	Active TSS	Brain Germinal Matrix	brain
15	chr3:98311000-98313200	Active TSS	Esophagus	oesophagus
16	chr3:98311000-98313200	Active TSS	HSMM	muscle
17	chr3:98311200-98313000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:98311200-98313000	Active TSS	Ovary	ovary
19	chr3:98311200-98313200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr3:98311200-98313200	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:98311400-98312800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:98311400-98312800	Active TSS	Fetal Intestine Small	intestine
23	chr3:98311400-98312800	Active TSS	HepG2	liver
24	chr3:98311400-98313000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:98311400-98313000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:98311400-98313000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:98311400-98313000	Active TSS	NHDF-Ad	bronchial
28	chr3:98311400-98313200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:98311400-98313200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:98311400-98313200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:98311400-98313200	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:98311400-98313200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:98311400-98313200	Active TSS	Fetal Intestine Large	intestine
34	chr3:98311400-98313200	Active TSS	Right Ventricle	heart
35	chr3:98311400-98313200	Active TSS	A549	lung
36	chr3:98311400-98313200	Active TSS	HMEC	breast
37	chr3:98311400-98313200	Active TSS	NHLF	lung
38	chr3:98311600-98312600	Active TSS	NHEK	skin
39	chr3:98311600-98312800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:98311600-98312800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:98311600-98313000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:98311600-98313000	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:98311600-98313000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:98311600-98313000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:98311600-98313000	Active TSS	Fetal Kidney	kidney
46	chr3:98311600-98313000	Active TSS	Gastric	stomach
47	chr3:98311600-98313000	Active TSS	Lung	lung
48	chr3:98311600-98313000	Active TSS	Pancreas	Pancrea
49	chr3:98311600-98313000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr3:98311600-98313000	Active TSS	HSMMtube	muscle

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