Variant report

Variant	rs28413725
Chromosome Location	chr3:46530685-46530686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr3:46530236-46530802	K562	blood:	n/a	n/a
2	ELF1	chr3:46530188-46530784	K562	blood:	n/a	n/a
3	RCOR1	chr3:46530162-46530780	Hela-S3	cervix:	n/a	n/a
4	PAX5	chr3:46530212-46530689	GM12878	blood:	n/a	n/a
5	EP300	chr3:46530245-46530712	HepG2	liver:	n/a	n/a
6	UBTF	chr3:46530215-46530689	K562	blood:	n/a	n/a
7	CTCF	chr3:46530139-46530880	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr3:46530164-46530801	ECC-1	luminal epithelium:	n/a	n/a
9	ELF1	chr3:46530211-46530806	GM12878	blood:	n/a	n/a
10	RAD21	chr3:46530125-46530768	IMR90	lung:	n/a	n/a
11	CHD1	chr3:46530077-46530738	IMR90	lung:	n/a	n/a
12	E2F6	chr3:46530241-46530724	K562	blood:	n/a	n/a
13	TEAD4	chr3:46530093-46530734	K562	blood:	n/a	n/a
14	RAD21	chr3:46530090-46530808	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr3:46530155-46530827	IMR90	lung:	n/a	n/a
16	CTCF	chr3:46530072-46530691	H1-hESC	embryonic stem cell:	n/a	n/a
17	SMC3	chr3:46530143-46530721	Hela-S3	cervix:	n/a	n/a
18	RXRA	chr3:46530122-46530725	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr3:46530109-46530696	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr3:46530192-46530688	MCF-7	breast:	n/a	n/a
21	MAX	chr3:46530073-46530696	A549	lung:	n/a	n/a
22	CTCF	chr3:46530121-46530847	IMR90	lung:	n/a	n/a
23	MYC	chr3:46530156-46530806	NB4	blood:	n/a	n/a
24	CTCF	chr3:46530043-46531002	A549	lung:	n/a	n/a
25	ELF1	chr3:46530239-46530691	K562	blood:	n/a	n/a
26	MAX	chr3:46530231-46530825	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr3:46530632-46530706	A549	lung:	n/a	n/a
28	RAD21	chr3:46530056-46530873	HCT-116	colon:	n/a	n/a
29	BHLHE40	chr3:46530177-46530760	K562	blood:	n/a	n/a
30	CTCF	chr3:46530631-46530702	ProgFib	skin:	n/a	n/a
31	RAD21	chr3:46530109-46530703	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F6	chr3:46530149-46530940	H1-hESC	embryonic stem cell:	n/a	n/a
33	SMC3	chr3:46530066-46530770	SK-N-SH	brain:	n/a	n/a
34	SMC3	chr3:46530129-46530745	K562	blood:	n/a	n/a
35	CBX3	chr3:46530140-46530695	HCT-116	colon:	n/a	n/a
36	CTCF	chr3:46530182-46530725	GM12892	blood:	n/a	n/a
37	ZNF263	chr3:46530190-46530746	HEK293-T-REx	kidney:	n/a	n/a
38	POLR2A	chr3:46530191-46531777	IMR90	lung:	n/a	n/a
39	SMC3	chr3:46530134-46530726	GM12878	blood:	n/a	n/a
40	TCF12	chr3:46530161-46530843	ECC-1	luminal epithelium:	n/a	n/a
41	TEAD4	chr3:46530212-46530951	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:46530659-46530700	GM12891	blood:	n/a	n/a
43	RAD21	chr3:46530076-46530862	H1-hESC	embryonic stem cell:	n/a	n/a
44	HMGN3	chr3:46530238-46531225	K562	blood:	n/a	n/a
45	POLR2A	chr3:46530515-46530789	MCF-7	breast:	n/a	n/a
46	CTCF	chr3:46530071-46530692	K562	blood:	n/a	n/a
47	E2F6	chr3:46530170-46530972	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr3:46530071-46530999	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr3:46530334-46530736	GM12892	blood:	n/a	n/a
50	MAX	chr3:46530162-46530741	NB4	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46529857..46530830-chr3:46549274..46550154,2	K562	blood:
2	chr1:121484254..121485268-chr3:46529887..46530781,3	MCF-7	breast:
3	chr3:46530293..46531287-chr3:46600917..46601700,2	K562	blood:
4	chr3:46530235..46530934-chr3:46606775..46607619,4	K562	blood:
5	chr3:46441887..46442673-chr3:46529916..46530717,2	K562	blood:
6	chr3:46490983..46491780-chr3:46529871..46530687,2	MCF-7	breast:
7	chr3:46529979..46530787-chr3:46607787..46608328,2	K562	blood:
8	chr3:46529944..46530794-chr3:46705110..46706015,2	K562	blood:
9	chr3:46530210..46534355-chr3:46598500..46601064,4	K562	blood:
10	chr3:46491080..46491922-chr3:46530287..46530830,3	MCF-7	breast:
11	chr3:46529686..46530942-chr3:46599020..46600485,46	MCF-7	breast:
12	chr3:46530210..46534355-chr3:46597750..46601064,4	K562	blood:
13	chr3:46528809..46531447-chr3:46546904..46549677,2	K562	blood:
14	chr3:46529871..46530872-chr3:46670590..46672462,23	K562	blood:
15	chr3:46529825..46532011-chr3:46599266..46600570,56	K562	blood:
16	chr3:46529884..46530839-chr3:46671105..46672532,19	MCF-7	breast:
17	chr3:46530490..46532908-chr3:46536819..46540385,3	K562	blood:
18	chr3:46529889..46530997-chr3:46599244..46600312,18	MCF-7	breast:
19	chr3:46529904..46530772-chr3:46603076..46604060,2	K562	blood:

No data

Variant related genes	Relation type
LTF	TF binding region
ENSG00000163825	Chromatin interaction
ENSG00000163827	Chromatin interaction
ENSG00000268324	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10514713	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130094	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714743	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719033	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489007	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490169	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496623	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496864	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1402151	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2037391	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139634	0.80[EUR][1000 genomes]
rs2280407	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934896	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60986461	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6763280	0.80[EUR][1000 genomes]
rs883739	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46529400-46534200	Enhancers	Dnd41	blood
2	chr3:46529800-46531200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr3:46530000-46531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:46530000-46531600	Enhancers	Fetal Thymus	thymus
5	chr3:46530000-46531800	Enhancers	NH-A	brain
6	chr3:46530200-46530800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr3:46530200-46530800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:46530200-46530800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr3:46530200-46530800	Enhancers	Brain Anterior Caudate	brain
10	chr3:46530200-46530800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr3:46530200-46530800	Enhancers	Placenta	Placenta
12	chr3:46530200-46530800	Bivalent Enhancer	Fetal Stomach	stomach
13	chr3:46530200-46530800	Genic enhancers	Right Atrium	heart
14	chr3:46530200-46531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:46530200-46531000	Enhancers	Fetal Intestine Large	intestine
16	chr3:46530200-46531000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:46530200-46531200	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:46530200-46531200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:46530200-46531200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:46530200-46531800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:46530200-46533800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:46530400-46530800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr3:46530400-46530800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:46530400-46530800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:46530400-46530800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:46530400-46530800	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr3:46530400-46530800	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr3:46530400-46530800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr3:46530400-46530800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr3:46530400-46530800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr3:46530400-46530800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr3:46530400-46530800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:46530400-46530800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:46530400-46530800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr3:46530400-46530800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:46530400-46530800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:46530400-46530800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:46530400-46530800	Flanking Active TSS	Liver	Liver
39	chr3:46530400-46530800	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr3:46530400-46530800	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr3:46530400-46530800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:46530400-46530800	Flanking Active TSS	Colonic Mucosa	Colon
43	chr3:46530400-46530800	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr3:46530400-46530800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr3:46530400-46530800	Bivalent/Poised TSS	Fetal Brain Female	brain
46	chr3:46530400-46530800	Enhancers	Pancreas	Pancrea
47	chr3:46530400-46530800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:46530400-46530800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:46530400-46530800	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr3:46530400-46530800	Flanking Active TSS	Thymus	Thymus

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