Variant report

Variant	rs552788391
Chromosome Location	chr13:52025775-52025776
allele	C/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	POLR2A	chr13:52025541-52025923	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr13:52025564-52026471	GM12878	blood:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
3	POLR2A	chr13:52025546-52028013	HCT-116	colon:	n/a	n/a
4	HEY1	chr13:52025211-52025876	K562	blood:	n/a	n/a
5	ELF1	chr13:52025518-52025805	K562	blood:	n/a	n/a
6	MAX	chr13:52025574-52026279	H1-hESC	embryonic stem cell:	n/a	n/a
7	YY1	chr13:52025493-52026262	SK-N-SH	brain:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
8	SIN3AK20	chr13:52025548-52025890	SK-N-SH	brain:	n/a	n/a
9	MAX	chr13:52025491-52026061	ECC-1	luminal epithelium:	n/a	n/a
10	TCF7L2	chr13:52025607-52025823	Hela-S3	cervix:	n/a	n/a
11	YY1	chr13:52025566-52026290	ECC-1	luminal epithelium:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
12	TAF1	chr13:52025664-52026453	HepG2	liver:	n/a	n/a
13	TAL1	chr13:52025280-52027330	K562	blood:	n/a	n/a
14	POLR2A	chr13:52025630-52028095	HEK293	kidney:	n/a	n/a
15	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
16	TAF1	chr13:52025611-52025861	H1-hESC	embryonic stem cell:	n/a	n/a
17	EP300	chr13:52025534-52026264	SK-N-SH	brain:	n/a	n/a
18	MXI1	chr13:52025599-52025949	Hela-S3	cervix:	n/a	n/a
19	CHD1	chr13:52024742-52028646	IMR90	lung:	n/a	n/a
20	MYC	chr13:52025635-52026244	MCF10A-Er-Src	breast:	n/a	n/a
21	CHD1	chr13:52025386-52028410	GM12878	blood:	n/a	n/a
22	CCNT2	chr13:52025623-52028030	K562	blood:	n/a	chr13:52027316-52027325 chr13:52025953-52025962 chr13:52027432-52027441
23	PBX3	chr13:52025482-52026098	SK-N-SH	brain:	n/a	chr13:52025765-52025774
24	CHD2	chr13:52025586-52026385	HepG2	liver:	n/a	n/a
25	POLR2A	chr13:52025562-52028409	H1-neurons	neurons:	n/a	n/a
26	MAX	chr13:52025612-52026328	Hela-S3	cervix:	n/a	n/a
27	MYC	chr13:52025727-52026475	MCF-7	breast:	n/a	n/a
28	POLR2A	chr13:52025530-52026304	HL-60	blood:	n/a	n/a
29	POLR2A	chr13:52025258-52028416	K562	blood:	n/a	n/a
30	TCF12	chr13:52025533-52026220	ECC-1	luminal epithelium:	n/a	n/a
31	GTF2F1	chr13:52025657-52026277	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr13:52025304-52026371	PBDE	blood:	n/a	n/a
33	POLR2A	chr13:52025371-52028505	GM18951	blood:	n/a	n/a
34	POLR2A	chr13:52025766-52026007	SK-N-SH	brain:	n/a	n/a
35	TAF1	chr13:52025560-52025789	GM12878	blood:	n/a	n/a
36	REST	chr13:52025376-52028611	H1-neurons	neurons:	n/a	chr13:52027338-52027356 chr13:52025635-52025644 chr13:52025993-52026006
37	POLR2A	chr13:52025569-52028397	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr13:52025590-52028395	MCF-7	breast:	n/a	n/a
39	NFIC	chr13:52025422-52025893	GM12878	blood:	n/a	n/a
40	POLR2A	chr13:52025428-52028620	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr13:52024109-52028486	GM18505	blood:	n/a	n/a
42	POLR2A	chr13:52025660-52028535	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr13:52025464-52026517	HepG2	liver:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
44	POLR2A	chr13:52025194-52025831	GM12891	blood:	n/a	n/a
45	POLR2A	chr13:52023653-52028418	HepG2	liver:	n/a	n/a
46	ZNF143	chr13:52025490-52026269	GM12878	blood:	n/a	chr13:52025791-52025810
47	PAX5	chr13:52025597-52026070	GM12892	blood:	n/a	n/a
48	MXI1	chr13:52025571-52025859	H1-hESC	embryonic stem cell:	n/a	n/a
49	YY1	chr13:52025632-52025981	GM12892	blood:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
50	TAF1	chr13:52025590-52026479	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149858264..149859990-chr13:52025489..52027316,2	MCF-7	breast:
2	chr13:52025774..52028487-chr13:52584807..52587141,2	K562	blood:
3	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
4	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
5	chr13:52022475..52029228-chr13:52156654..52162250,29	K562	blood:
6	chr13:51933288..51938259-chr13:52024808..52026901,4	K562	blood:
7	chr13:52025554..52026127-chr17:8286258..8286976,2	Hela-S3	cervix:
8	chr12:29302116..29302733-chr13:52025571..52026304,2	NB4	blood:
9	chr13:51996691..52002238-chr13:52025569..52028541,7	MCF-7	breast:
10	chr13:52025248..52027565-chr13:52113097..52117557,5	K562	blood:
11	chr13:52025577..52029967-chr13:52343918..52348772,7	MCF-7	breast:
12	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:
13	chr13:52025241..52027687-chr13:52171016..52174536,3	MCF-7	breast:
14	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
15	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
16	chr13:52023587..52026212-chr20:45985508..45987866,2	MCF-7	breast:
17	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
18	chr13:51994030..51996463-chr13:52024763..52027853,3	MCF-7	breast:
19	chr13:52025027..52027980-chr2:128047526..128049328,2	MCF-7	breast:
20	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
21	chr13:52024964..52027210-chr3:57581929..57583601,2	MCF-7	breast:
22	chr13:52025248..52026911-chr13:52113097..52115719,3	K562	blood:
23	chr13:52025709..52029684-chr13:52361886..52365561,3	MCF-7	breast:
24	chr13:52025134..52027888-chr13:53029090..53030597,2	MCF-7	breast:
25	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
26	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
27	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
28	chr13:52025316..52028305-chr18:3447499..3449683,2	MCF-7	breast:
29	chr13:52024180..52026043-chr13:52139073..52141757,2	K562	blood:
30	chr13:52025411..52028275-chr17:56707657..56710350,3	MCF-7	breast:
31	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
32	chr13:52025591..52028718-chr13:52111998..52119680,9	MCF-7	breast:
33	chr13:52025527..52027084-chr13:52138971..52141023,2	MCF-7	breast:
34	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:

Variant related genes	Relation type
INTS6	TF binding region
INTS6-AS1	TF binding region
RPS4XP16	TF binding region
ENSG00000269965	Chromatin interaction
ENSG00000161970	Chromatin interaction
ENSG00000123191	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000224451	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000168374	Chromatin interaction
ENSG00000272146	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000252141	Chromatin interaction
ENSG00000270101	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000253710	Chromatin interaction
ENSG00000263809	Chromatin interaction
ENSG00000136108	Chromatin interaction
ENSG00000064763	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3421830	chr13:52024776-52027324	Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv3360115	chr13:52025676-52027974	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 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	chr13:52024400-52028200	Active TSS	Thymus	Thymus
2	chr13:52024800-52025800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr13:52024800-52026600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:52024800-52027200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:52025000-52025800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr13:52025000-52025800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr13:52025000-52025800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr13:52025000-52025800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr13:52025000-52025800	Active TSS	Right Atrium	heart
10	chr13:52025000-52028000	Active TSS	Hela-S3	cervix
11	chr13:52025000-52028000	Active TSS	HMEC	breast
12	chr13:52025000-52028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr13:52025000-52028200	Active TSS	Primary T cells fromperipheralblood	blood
14	chr13:52025000-52028200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr13:52025000-52028600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr13:52025000-52028600	Active TSS	Right Ventricle	heart
17	chr13:52025000-52028800	Active TSS	Fetal Muscle Leg	muscle
18	chr13:52025000-52028800	Active TSS	K562	blood
19	chr13:52025000-52029000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:52025000-52029000	Active TSS	GM12878-XiMat	blood
21	chr13:52025200-52025800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr13:52025200-52025800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr13:52025200-52025800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr13:52025200-52025800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr13:52025200-52027200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:52025200-52028000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:52025200-52028000	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr13:52025200-52028000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:52025200-52028000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr13:52025200-52028000	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr13:52025200-52028000	Active TSS	NHLF	lung
32	chr13:52025200-52028200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr13:52025200-52028200	Active TSS	Brain Cingulate Gyrus	brain
34	chr13:52025200-52028200	Active TSS	Stomach Smooth Muscle	stomach
35	chr13:52025200-52028200	Active TSS	HSMMtube	muscle
36	chr13:52025200-52028400	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr13:52025200-52028600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr13:52025200-52028600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr13:52025200-52028600	Active TSS	H9 Cell Line	embryonic stem cell
40	chr13:52025200-52028600	Active TSS	Aorta	Aorta
41	chr13:52025200-52028600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr13:52025200-52028600	Active TSS	Fetal Muscle Trunk	muscle
43	chr13:52025200-52028600	Active TSS	Lung	lung
44	chr13:52025200-52028600	Active TSS	A549	lung
45	chr13:52025200-52028800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:52025200-52028800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:52025200-52028800	Active TSS	Fetal Intestine Small	intestine
48	chr13:52025200-52028800	Active TSS	Fetal Thymus	thymus
49	chr13:52025200-52028800	Active TSS	Psoas Muscle	Psoas
50	chr13:52025200-52028800	Active TSS	NHDF-Ad	bronchial

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