Variant report

Variant	rs560891120
Chromosome Location	chr4:56261763-56261764
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	MAFK	chr4:56261482-56262274	Hela-S3	cervix:	n/a	n/a
2	HDAC2	chr4:56261509-56262138	HepG2	liver:	n/a	chr4:56261622-56261636
3	POLR2A	chr4:56261620-56262356	A549	lung:	n/a	n/a
4	E2F4	chr4:56261555-56262236	MCF10A-Er-Src	breast:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262136-56262146
5	MAX	chr4:56261475-56262910	HepG2	liver:	n/a	chr4:56261670-56261680
6	POLR2A	chr4:56261418-56262619	PFSK-1	brain:	n/a	n/a
7	MAX	chr4:56261350-56262354	MCF-7	breast:	n/a	chr4:56261670-56261680
8	YY1	chr4:56261565-56262808	GM12878	blood:	n/a	chr4:56262663-56262674 chr4:56262248-56262257 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56261904-56261918 chr4:56262246-56262257 chr4:56262245-56262254
9	E2F4	chr4:56261590-56262783	K562	blood:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
10	CTCF	chr4:56261680-56261830	GM12870	blood:	n/a	n/a
11	POLR2A	chr4:56261604-56262358	HCT-116	colon:	n/a	n/a
12	REST	chr4:56261562-56261790	Hela-S3	cervix:	n/a	n/a
13	HEY1	chr4:56261581-56262393	K562	blood:	n/a	chr4:56262325-56262340 chr4:56262103-56262118 chr4:56261904-56261919
14	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
15	SIN3AK20	chr4:56261474-56262514	MCF-7	breast:	n/a	n/a
16	RAD21	chr4:56261464-56262288	IMR90	lung:	n/a	n/a
17	POLR2A	chr4:56261568-56262455	HCT-116	colon:	n/a	n/a
18	POLR2A	chr4:56261482-56262483	U87	brain:	n/a	n/a
19	TCF12	chr4:56261565-56262891	ECC-1	luminal epithelium:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
20	MYC	chr4:56261682-56262133	GM12878	blood:	n/a	n/a
21	YY1	chr4:56261630-56262335	ECC-1	luminal epithelium:	n/a	chr4:56262248-56262257 chr4:56262166-56262177 chr4:56262243-56262254 chr4:56261904-56261918 chr4:56262246-56262257 chr4:56262245-56262254
22	MAFK	chr4:56261479-56262088	K562	blood:	n/a	n/a
23	MAX	chr4:56261385-56262415	A549	lung:	n/a	chr4:56261670-56261680
24	CTCF	chr4:56261660-56261810	GM12865	blood:	n/a	n/a
25	POLR2A	chr4:56261662-56262375	HEK293	kidney:	n/a	n/a
26	POLR2A	chr4:56261613-56262500	ECC-1	luminal epithelium:	n/a	n/a
27	TBP	chr4:56261474-56262301	GM12878	blood:	n/a	n/a
28	IRF1	chr4:56261495-56262351	K562	blood:	n/a	n/a
29	TAF1	chr4:56261625-56262821	HepG2	liver:	n/a	n/a
30	TAF1	chr4:56261651-56262352	PFSK-1	brain:	n/a	n/a
31	EP300	chr4:56261563-56262485	ECC-1	luminal epithelium:	n/a	chr4:56262323-56262339 chr4:56262247-56262256 chr4:56262136-56262145 chr4:56261845-56261859 chr4:56262313-56262322 chr4:56262192-56262208 chr4:56262244-56262253
32	CREB1	chr4:56261492-56262464	GM12878	blood:	n/a	chr4:56261747-56261760
33	ZEB1	chr4:56261454-56262885	HepG2	liver:	n/a	n/a
34	MYC	chr4:56261571-56262098	MCF10A-Er-Src	breast:	n/a	chr4:56261670-56261680
35	MAX	chr4:56261507-56262208	A549	lung:	n/a	chr4:56261670-56261680
36	TCF12	chr4:56261674-56262425	A549	lung:	n/a	chr4:56262001-56262008 chr4:56262115-56262122
37	HMGN3	chr4:56261567-56263107	K562	blood:	n/a	n/a
38	POLR2A	chr4:56261530-56263279	ProgFib	skin:	n/a	n/a
39	RFX5	chr4:56261217-56262273	Hela-S3	cervix:	n/a	n/a
40	RCOR1	chr4:56261457-56262289	Hela-S3	cervix:	n/a	n/a
41	MAX	chr4:56261305-56262333	ECC-1	luminal epithelium:	n/a	chr4:56261670-56261680
42	BACH1	chr4:56261513-56261799	K562	blood:	n/a	n/a
43	MAX	chr4:56261226-56263609	NB4	blood:	n/a	chr4:56261670-56261680
44	POLR2A	chr4:56261396-56262912	HepG2	liver:	n/a	n/a
45	CHD2	chr4:56261758-56262848	K562	blood:	n/a	n/a
46	POLR2A	chr4:56261529-56263721	Hela-S3	cervix:	n/a	n/a
47	MAX	chr4:56261342-56262462	HCT-116	colon:	n/a	chr4:56261670-56261680
48	POU2F2	chr4:56261576-56262301	GM12891	blood:	n/a	chr4:56261582-56261595 chr4:56262086-56262098
49	E2F6	chr4:56261300-56262493	H1-hESC	embryonic stem cell:	n/a	chr4:56261948-56261958 chr4:56261658-56261665 chr4:56262243-56262253 chr4:56262136-56262146 chr4:56262246-56262256
50	POLR2A	chr4:56261539-56262979	GM15510	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:56261753-56261803	ProgFib	skin:	n/a
2	chr4:56261753-56261803	MCF10A-Er-Src	breast:	n/a
3	chr4:56261753-56261803	GM12892	blood:	n/a
4	chr4:56261753-56261803	AoSMC	blood vessel:	n/a
5	chr4:56261753-56261803	HRE	kidney:	n/a
6	chr4:56261753-56261803	U87	brain:	n/a
7	chr4:56261753-56261803	AG09309	skin:	n/a
8	chr4:56261753-56261803	HL-60	blood:	n/a
9	chr4:56261753-56261803	HAEpiC	amniotic membrane:	n/a
10	chr4:56261753-56261803	HCPEpiC	choroid plexus:	n/a
11	chr4:56261753-56261803	HRCEpiC	kidney:	n/a
12	chr4:56261753-56261803	NHDF-neo	bronchial:	n/a
13	chr4:56261753-56261803	HEK293	kidney:	embryo
14	chr4:56261753-56261803	Hela-S3	cervix:	n/a
15	chr4:56261753-56261803	AG09319	gingival:	n/a
16	chr4:56261753-56261803	Caco-2	colon:	n/a
17	chr4:56261753-56261803	AG10803	skin:	n/a
18	chr4:56261753-56261803	ECC-1	luminal epithelium:	n/a
19	chr4:56261753-56261803	Hepatocyte	liver:	n/a
20	chr4:56261753-56261803	NHBE	bronchial:	n/a
21	chr4:56261753-56261803	HUVEC	blood vessel:	n/a
22	chr4:56261753-56261803	GM12891	blood:	n/a
23	chr4:56261753-56261803	PANC-1	pancreas:	n/a
24	chr4:56261753-56261803	CMK	blood:	n/a
25	chr4:56261753-56261803	SK-N-SH	brain:	n/a
26	chr4:56261753-56261803	GM12878	blood:	n/a
27	chr4:56261753-56261803	T-47D	breast:	n/a
28	chr4:56261753-56261803	HIPEpiC	eye:	n/a
29	chr4:56261753-56261803	NT2-D1	testis:	n/a
30	chr4:56261753-56261803	HPAEpiC	pulmonary alveolar:	n/a
31	chr4:56261753-56261803	PFSK-1	brain:	n/a
32	chr4:56261753-56261803	NB4	blood:	n/a
33	chr4:56261753-56261803	HNPCEpiC	eye:	n/a
34	chr4:56261753-56261803	BJ	skin:	n/a
35	chr4:56261753-56261803	HCF	heart:	n/a
36	chr4:56261753-56261803	GM06990	blood:	n/a
37	chr4:56261753-56261803	AG04450	lung:	fetal
38	chr4:56261753-56261803	ovcar-3	ovarian:	n/a
39	chr4:56261753-56261803	AG04449	skin:	fetal
40	chr4:56261753-56261803	NH-A	brain:	n/a
41	chr4:56261753-56261803	BE2_C	brain:	n/a
42	chr4:56261753-56261803	IMR90	lung:	fetal
43	chr4:56261753-56261803	HCM	heart:	n/a
44	chr4:56261753-56261803	MCF-7	breast:	n/a
45	chr4:56261753-56261803	HepG2	liver:	n/a
46	chr4:56261753-56261803	HCT-116	colon:	n/a
47	chr4:56261753-56261803	SAEC	small airway:	n/a
48	chr4:56261753-56261803	HRPEpiC	eye:	n/a
49	chr4:56261753-56261803	K562	blood:	n/a
50	chr4:56261753-56261803	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr3:150125609..150126516-chr4:56261520..56262416,2	HCT-116	colon:
3	chr4:56222050..56228109-chr4:56258616..56264786,10	MCF-7	breast:
4	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
5	chr4:56245537..56248832-chr4:56260791..56264132,6	MCF-7	breast:
6	chr4:56252554..56257772-chr4:56259709..56263846,8	MCF-7	breast:
7	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
8	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
9	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
10	chr4:56260988..56264413-chr4:56410743..56414640,3	K562	blood:
11	chr4:56248184..56250642-chr4:56260280..56262635,2	K562	blood:
12	chr19:3985082..3985890-chr4:56261509..56262195,2	Hela-S3	cervix:
13	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
14	chr16:67313002..67313543-chr4:56261724..56262428,2	NB4	blood:

Variant related genes	Relation type
TMEM165	TF binding region
TMEM165	CpG island
ENSG00000134852	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000251111	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000196155	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000167658	Chromatin interaction
ENSG00000273257	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv3440757	chr4:56261420-56263968	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56261200-56261800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr4:56261200-56261800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr4:56261200-56261800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr4:56261200-56261800	Flanking Active TSS	HepG2	liver
5	chr4:56261200-56261800	Flanking Active TSS	HUVEC	blood vessel
6	chr4:56261200-56261800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr4:56261200-56262000	Active TSS	Fetal Brain Male	brain
8	chr4:56261200-56262600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr4:56261200-56263000	Active TSS	Fetal Brain Female	brain
10	chr4:56261200-56263400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:56261200-56263400	Active TSS	Osteobl	bone
12	chr4:56261200-56264800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr4:56261200-56265200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:56261400-56261800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:56261400-56261800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr4:56261400-56261800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr4:56261400-56261800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr4:56261400-56261800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr4:56261400-56261800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr4:56261400-56261800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr4:56261400-56261800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:56261400-56261800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr4:56261400-56261800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:56261400-56261800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr4:56261400-56261800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr4:56261400-56261800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr4:56261400-56261800	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr4:56261400-56261800	Flanking Active TSS	Fetal Lung	lung
29	chr4:56261400-56261800	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr4:56261400-56261800	Flanking Active TSS	Placenta	Placenta
31	chr4:56261400-56261800	Flanking Active TSS	Fetal Thymus	thymus
32	chr4:56261400-56261800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr4:56261400-56261800	Enhancers	Small Intestine	intestine
34	chr4:56261400-56261800	Flanking Active TSS	Thymus	Thymus
35	chr4:56261400-56261800	Flanking Active TSS	Dnd41	blood
36	chr4:56261400-56261800	Flanking Active TSS	HMEC	breast
37	chr4:56261400-56262000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:56261400-56262000	Flanking Active TSS	Liver	Liver
39	chr4:56261400-56262000	Active TSS	Fetal Heart	heart
40	chr4:56261400-56262000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr4:56261400-56262400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:56261400-56262800	Active TSS	Primary T cells from cord blood	blood
43	chr4:56261400-56262800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr4:56261400-56263000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:56261400-56263000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr4:56261400-56263200	Active TSS	Brain Germinal Matrix	brain
47	chr4:56261400-56263200	Active TSS	Colonic Mucosa	Colon
48	chr4:56261400-56263200	Active TSS	Fetal Stomach	stomach
49	chr4:56261400-56263400	Active TSS	HSMM	muscle
50	chr4:56261400-56263600	Active TSS	Brain Substantia Nigra	brain

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