Variant report

Variant	rs28370006
Chromosome Location	chr1:223899898-223899899
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	RAD21	chr1:223899618-223900465	HCT-116	colon:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
2	TCF12	chr1:223899452-223900449	A549	lung:	n/a	chr1:223899873-223899883
3	ELF1	chr1:223899799-223900328	K562	blood:	n/a	chr1:223900239-223900251 chr1:223900230-223900242
4	CTCF	chr1:223899780-223899930	GM12865	blood:	n/a	n/a
5	ZNF143	chr1:223899595-223900405	K562	blood:	n/a	chr1:223900038-223900048 chr1:223900230-223900240 chr1:223900039-223900049
6	JUND	chr1:223899525-223900640	SK-N-SH	brain:	n/a	chr1:223900208-223900219
7	MXI1	chr1:223899837-223900480	GM12878	blood:	n/a	n/a
8	YY1	chr1:223899844-223900573	K562	blood:	n/a	chr1:223900184-223900198 chr1:223900229-223900238
9	POLR2A	chr1:223899878-223900570	HUVEC	blood vessel:	n/a	n/a
10	RAD21	chr1:223899865-223900268	HepG2	liver:	n/a	chr1:223900071-223900084 chr1:223900073-223900085
11	RAD21	chr1:223899831-223900260	HepG2	liver:	n/a	chr1:223900071-223900084 chr1:223900073-223900085
12	POLR2A	chr1:223899527-223902278	U87	brain:	n/a	n/a
13	GTF2F1	chr1:223899864-223900209	K562	blood:	n/a	n/a
14	RAD21	chr1:223899891-223900268	A549	lung:	n/a	chr1:223900071-223900084 chr1:223900073-223900085
15	POLR2A	chr1:223899728-223901800	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr1:223899560-223901728	K562	blood:	n/a	n/a
17	YY1	chr1:223899838-223900532	H1-hESC	embryonic stem cell:	n/a	chr1:223900184-223900198 chr1:223900229-223900238
18	TCF7L2	chr1:223899785-223900444	HCT-116	colon:	n/a	n/a
19	RAD21	chr1:223899365-223901256	SK-N-SH	brain:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
20	RAD21	chr1:223899769-223900631	H1-hESC	embryonic stem cell:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
21	CTCF	chr1:223899847-223900339	A549	lung:	n/a	n/a
22	SIN3AK20	chr1:223899830-223900537	SK-N-SH	brain:	n/a	n/a
23	WRNIP1	chr1:223899710-223899969	GM12878	blood:	n/a	n/a
24	RAD21	chr1:223899803-223900367	ECC-1	luminal epithelium:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
25	HEY1	chr1:223899856-223900540	K562	blood:	n/a	chr1:223900251-223900266 chr1:223900271-223900286 chr1:223900258-223900273 chr1:223900143-223900158
26	POLR2A	chr1:223899885-223901918	Hela-S3	cervix:	n/a	n/a
27	RAD21	chr1:223899885-223900254	GM12878	blood:	n/a	chr1:223900071-223900084 chr1:223900073-223900085
28	POLR2A	chr1:223899498-223900520	PANC-1	pancreas:	n/a	n/a
29	YY1	chr1:223899839-223900600	GM12892	blood:	n/a	chr1:223900184-223900198 chr1:223900229-223900238
30	KAP1	chr1:223899586-223900520	HEK293	kidney:	n/a	n/a
31	CTCF	chr1:223899840-223900390	K562	blood:	n/a	n/a
32	REST	chr1:223899637-223900270	A549	lung:	n/a	chr1:223900161-223900171 chr1:223900059-223900069 chr1:223900063-223900072
33	CCNT2	chr1:223899848-223901156	K562	blood:	n/a	n/a
34	POLR2A	chr1:223899689-223900971	HEK293	kidney:	n/a	n/a
35	MYC	chr1:223899805-223900310	MCF10A-Er-Src	breast:	n/a	n/a
36	TBL1XR1	chr1:223899570-223900324	K562	blood:	n/a	n/a
37	RAD21	chr1:223899886-223900359	K562	blood:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
38	CBX3	chr1:223899367-223900587	K562	blood:	n/a	n/a
39	RAD21	chr1:223899889-223900528	H1-hESC	embryonic stem cell:	n/a	chr1:223900071-223900084 chr1:223900073-223900085 chr1:223900278-223900291
40	POLR2A	chr1:223898708-223906948	U87	brain:	n/a	n/a
41	ETS1	chr1:223899893-223900377	K562	blood:	n/a	n/a
42	SMC3	chr1:223899898-223900479	K562	blood:	n/a	n/a
43	CTCF	chr1:223899867-223900223	HepG2	liver:	n/a	n/a
44	CHD2	chr1:223899795-223900565	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr1:223899575-223902247	HCT-116	colon:	n/a	n/a
46	JUND	chr1:223899720-223900579	K562	blood:	n/a	chr1:223900208-223900219
47	RUNX3	chr1:223899880-223900114	GM12878	blood:	n/a	n/a
48	CREB1	chr1:223899807-223900684	A549	lung:	n/a	n/a
49	ZNF143	chr1:223899863-223900490	GM12878	blood:	n/a	chr1:223900038-223900048 chr1:223900230-223900240 chr1:223900039-223900049
50	MYC	chr1:223899666-223901153	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:223899853-223899903	NB4	blood:	n/a
2	chr1:223899853-223899903	U87	brain:	n/a
3	chr1:223899853-223899903	SKMC	muscle:	n/a
4	chr1:223899853-223899903	ProgFib	skin:	n/a
5	chr1:223899853-223899903	BJ	skin:	n/a
6	chr1:223899853-223899903	NT2-D1	testis:	n/a
7	chr1:223899853-223899903	MCF10A-Er-Src	breast:	n/a
8	chr1:223899853-223899903	SK-N-SH	brain:	n/a
9	chr1:223899853-223899903	GM12891	blood:	n/a
10	chr1:223899853-223899903	PANC-1	pancreas:	n/a
11	chr1:223899853-223899903	HepG2	liver:	n/a
12	chr1:223899853-223899903	Hela-S3	cervix:	n/a
13	chr1:223899853-223899903	HNPCEpiC	eye:	n/a
14	chr1:223899853-223899903	MCF-7	breast:	n/a
15	chr1:223899853-223899903	HEEpiC	esophagus:	n/a
16	chr1:223899853-223899903	RPTEC	kidney:	n/a
17	chr1:223899853-223899903	K562	blood:	n/a
18	chr1:223899853-223899903	HAEpiC	amniotic membrane:	n/a
19	chr1:223899853-223899903	Hepatocyte	liver:	n/a
20	chr1:223899853-223899903	GM06990	blood:	n/a
21	chr1:223899853-223899903	Caco-2	colon:	n/a
22	chr1:223899853-223899903	HRPEpiC	eye:	n/a
23	chr1:223899853-223899903	AG09309	skin:	n/a
24	chr1:223899853-223899903	Jurkat	blood:	n/a
25	chr1:223899853-223899903	CMK	blood:	n/a
26	chr1:223899853-223899903	H1-hESC	embryonic stem cell:	embryo
27	chr1:223899853-223899903	HCT-116	colon:	n/a
28	chr1:223899853-223899903	HRE	kidney:	n/a
29	chr1:223899853-223899903	LNCaP	prostate:	n/a
30	chr1:223899853-223899903	HL-60	blood:	n/a
31	chr1:223899853-223899903	HCF	heart:	n/a
32	chr1:223899853-223899903	HEK293	kidney:	embryo
33	chr1:223899853-223899903	NHBE	bronchial:	n/a
34	chr1:223899853-223899903	NH-A	brain:	n/a
35	chr1:223899853-223899903	PFSK-1	brain:	n/a
36	chr1:223899853-223899903	HPAEpiC	pulmonary alveolar:	n/a
37	chr1:223899853-223899903	GM12892	blood:	n/a
38	chr1:223899853-223899903	HCM	heart:	n/a
39	chr1:223899853-223899903	HUVEC	blood vessel:	n/a
40	chr1:223899853-223899903	AG04450	lung:	fetal
41	chr1:223899853-223899903	SK-N-SH_RA	brain:	n/a
42	chr1:223899853-223899903	AoSMC	blood vessel:	n/a
43	chr1:223899853-223899903	ECC-1	luminal epithelium:	n/a
44	chr1:223899853-223899903	IMR90	lung:	fetal
45	chr1:223899853-223899903	NHDF-neo	bronchial:	n/a
46	chr1:223899853-223899903	HMEC	breast:	n/a
47	chr1:223899853-223899903	AG09319	gingival:	n/a
48	chr1:223899853-223899903	SK-N-MC	brain:	n/a
49	chr1:223899853-223899903	PrEC	prostate:	n/a
50	chr1:223899853-223899903	T-47D	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223886668..223890344-chr1:223897746..223900327,3	K562	blood:
2	chr1:223899719..223901460-chr1:224517221..224519970,2	K562	blood:
3	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
4	chr1:223882393..223884567-chr1:223898139..223900023,2	MCF-7	breast:
5	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
6	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
7	chr1:223899719..223902673-chr1:224516675..224518721,2	K562	blood:
8	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
9	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:

Variant related genes	Relation type
CAPN2	TF binding region
CAPN2	CpG island
ENSG00000143514	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	esv3344542	chr1:223899354-223901902	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	12 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	chr1:223889000-223900000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:223896000-223900000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:223896000-223900200	Weak transcription	Small Intestine	intestine
4	chr1:223897200-223900000	Weak transcription	Lung	lung
5	chr1:223897600-223900200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:223899400-223900000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr1:223899400-223900000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr1:223899400-223900000	Flanking Active TSS	Hela-S3	cervix
9	chr1:223899400-223901400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:223899600-223900000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:223899600-223900000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:223899600-223900000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:223899600-223900000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:223899600-223900000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr1:223899600-223900000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:223899600-223900000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:223899600-223900000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:223899600-223900000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr1:223899600-223900000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr1:223899600-223900000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:223899600-223900000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr1:223899600-223900000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:223899600-223900000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr1:223899600-223900000	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr1:223899600-223900000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:223899600-223900000	Flanking Active TSS	Colonic Mucosa	Colon
27	chr1:223899600-223900000	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr1:223899600-223900000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:223899600-223900000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:223899600-223900000	Enhancers	Right Ventricle	heart
31	chr1:223899600-223900000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr1:223899600-223900000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr1:223899600-223900000	Flanking Active TSS	Stomach Mucosa	stomach
34	chr1:223899600-223900000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr1:223899600-223900000	Weak transcription	Spleen	Spleen
36	chr1:223899600-223900000	Flanking Active TSS	A549	lung
37	chr1:223899600-223900000	Flanking Active TSS	HMEC	breast
38	chr1:223899600-223900000	Flanking Active TSS	HSMM	muscle
39	chr1:223899600-223900000	Flanking Active TSS	K562	blood
40	chr1:223899600-223900000	Flanking Active TSS	NHDF-Ad	bronchial
41	chr1:223899600-223900000	Flanking Active TSS	NHEK	skin
42	chr1:223899600-223900000	Flanking Active TSS	NHLF	lung
43	chr1:223899600-223900000	Flanking Active TSS	Osteobl	bone
44	chr1:223899600-223900200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:223899600-223900200	Flanking Active TSS	GM12878-XiMat	blood
46	chr1:223899600-223900400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:223899600-223900400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:223899600-223900600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr1:223899600-223901000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr1:223899600-223901000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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