Variant report

Variant	rs544088296
Chromosome Location	chr13:52025954-52025955
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	ZNF384	chr13:52025830-52026130	K562	blood:	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	MAX	chr13:52025574-52026279	H1-hESC	embryonic stem cell:	n/a	n/a
5	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
6	MAX	chr13:52025491-52026061	ECC-1	luminal epithelium:	n/a	n/a
7	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
8	TAF1	chr13:52025664-52026453	HepG2	liver:	n/a	n/a
9	TAL1	chr13:52025280-52027330	K562	blood:	n/a	n/a
10	POLR2A	chr13:52025630-52028095	HEK293	kidney:	n/a	n/a
11	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
12	EP300	chr13:52025534-52026264	SK-N-SH	brain:	n/a	n/a
13	CHD1	chr13:52024742-52028646	IMR90	lung:	n/a	n/a
14	RAD21	chr13:52025861-52026238	SK-N-SH_RA	brain:	n/a	n/a
15	MYC	chr13:52025635-52026244	MCF10A-Er-Src	breast:	n/a	n/a
16	CHD1	chr13:52025386-52028410	GM12878	blood:	n/a	n/a
17	CCNT2	chr13:52025623-52028030	K562	blood:	n/a	chr13:52027316-52027325 chr13:52025953-52025962 chr13:52027432-52027441
18	EGR1	chr13:52025863-52026558	K562	blood:	n/a	chr13:52025954-52025967 chr13:52025953-52025968
19	PBX3	chr13:52025482-52026098	SK-N-SH	brain:	n/a	chr13:52025765-52025774
20	CHD2	chr13:52025586-52026385	HepG2	liver:	n/a	n/a
21	POLR2A	chr13:52025562-52028409	H1-neurons	neurons:	n/a	n/a
22	MAX	chr13:52025612-52026328	Hela-S3	cervix:	n/a	n/a
23	MYC	chr13:52025727-52026475	MCF-7	breast:	n/a	n/a
24	POLR2A	chr13:52025530-52026304	HL-60	blood:	n/a	n/a
25	POLR2A	chr13:52025258-52028416	K562	blood:	n/a	n/a
26	TCF12	chr13:52025533-52026220	ECC-1	luminal epithelium:	n/a	n/a
27	GTF2F1	chr13:52025657-52026277	Hela-S3	cervix:	n/a	n/a
28	CHD2	chr13:52025789-52026197	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr13:52025304-52026371	PBDE	blood:	n/a	n/a
30	POLR2A	chr13:52025371-52028505	GM18951	blood:	n/a	n/a
31	POLR2A	chr13:52025766-52026007	SK-N-SH	brain:	n/a	n/a
32	REST	chr13:52025376-52028611	H1-neurons	neurons:	n/a	chr13:52027338-52027356 chr13:52025635-52025644 chr13:52025993-52026006
33	POLR2A	chr13:52025569-52028397	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr13:52025590-52028395	MCF-7	breast:	n/a	n/a
35	POLR2A	chr13:52025428-52028620	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr13:52024109-52028486	GM18505	blood:	n/a	n/a
37	POLR2A	chr13:52025660-52028535	H1-hESC	embryonic stem cell:	n/a	n/a
38	YY1	chr13:52025464-52026517	HepG2	liver:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
39	POLR2A	chr13:52023653-52028418	HepG2	liver:	n/a	n/a
40	ZNF143	chr13:52025490-52026269	GM12878	blood:	n/a	chr13:52025791-52025810
41	PAX5	chr13:52025597-52026070	GM12892	blood:	n/a	n/a
42	YY1	chr13:52025632-52025981	GM12892	blood:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
43	TAF1	chr13:52025590-52026479	H1-neurons	neurons:	n/a	n/a
44	TBP	chr13:52025349-52026368	K562	blood:	n/a	n/a
45	JUND	chr13:52025793-52026227	K562	blood:	n/a	n/a
46	POLR2A	chr13:52025620-52028387	K562	blood:	n/a	n/a
47	POLR2A	chr13:52025901-52028516	GM12891	blood:	n/a	n/a
48	POLR2A	chr13:52025917-52026448	HUVEC	blood vessel:	n/a	n/a
49	MTA3	chr13:52025208-52028795	GM12878	blood:	n/a	n/a
50	POLR2A	chr13:52025507-52028083	ECC-1	luminal epithelium:	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	chr13:52025793..52028352-chr13:52043580..52045211,2	MCF-7	breast:
9	chr12:29302116..29302733-chr13:52025571..52026304,2	NB4	blood:
10	chr13:51996691..52002238-chr13:52025569..52028541,7	MCF-7	breast:
11	chr13:52025778..52026371-chr17:79790811..79791764,2	HCT-116	colon:
12	chr13:52025794..52034237-chr13:52040132..52048046,20	K562	blood:
13	chr13:52025248..52027565-chr13:52113097..52117557,5	K562	blood:
14	chr13:52025577..52029967-chr13:52343918..52348772,7	MCF-7	breast:
15	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:
16	chr13:52025241..52027687-chr13:52171016..52174536,3	MCF-7	breast:
17	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
18	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
19	chr13:52023587..52026212-chr20:45985508..45987866,2	MCF-7	breast:
20	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
21	chr13:51994030..51996463-chr13:52024763..52027853,3	MCF-7	breast:
22	chr13:52025027..52027980-chr2:128047526..128049328,2	MCF-7	breast:
23	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
24	chr13:52024964..52027210-chr3:57581929..57583601,2	MCF-7	breast:
25	chr13:52025248..52026911-chr13:52113097..52115719,3	K562	blood:
26	chr13:52025709..52029684-chr13:52361886..52365561,3	MCF-7	breast:
27	chr13:52025134..52027888-chr13:53029090..53030597,2	MCF-7	breast:
28	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
29	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
30	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
31	chr13:52025316..52028305-chr18:3447499..3449683,2	MCF-7	breast:
32	chr13:52024180..52026043-chr13:52139073..52141757,2	K562	blood:
33	chr13:52025411..52028275-chr17:56707657..56710350,3	MCF-7	breast:
34	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
35	chr13:52025591..52028718-chr13:52111998..52119680,9	MCF-7	breast:
36	chr13:52025527..52027084-chr13:52138971..52141023,2	MCF-7	breast:
37	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:

Variant related genes	Relation type
INTS6-AS1	TF binding region
RPS4XP16	TF binding region
INTS6	TF binding region
ENSG00000231856	Chromatin interaction
ENSG00000253710	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000161970	Chromatin interaction
ENSG00000270101	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000272146	Chromatin interaction
ENSG00000225663	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000269965	Chromatin interaction
ENSG00000168374	Chromatin interaction
ENSG00000252141	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000123191	Chromatin interaction
ENSG00000064763	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000243900	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000263809	Chromatin interaction
ENSG00000229906	Chromatin interaction
ENSG00000206920	Chromatin interaction
ENSG00000224451	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000136108	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	chr13:52024800-52026600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:52024800-52027200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr13:52025000-52028000	Active TSS	Hela-S3	cervix
5	chr13:52025000-52028000	Active TSS	HMEC	breast
6	chr13:52025000-52028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr13:52025000-52028200	Active TSS	Primary T cells fromperipheralblood	blood
8	chr13:52025000-52028200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr13:52025000-52028600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr13:52025000-52028600	Active TSS	Right Ventricle	heart
11	chr13:52025000-52028800	Active TSS	Fetal Muscle Leg	muscle
12	chr13:52025000-52028800	Active TSS	K562	blood
13	chr13:52025000-52029000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:52025000-52029000	Active TSS	GM12878-XiMat	blood
15	chr13:52025200-52027200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr13:52025200-52028000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:52025200-52028000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr13:52025200-52028000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:52025200-52028000	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr13:52025200-52028000	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr13:52025200-52028000	Active TSS	NHLF	lung
22	chr13:52025200-52028200	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr13:52025200-52028200	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:52025200-52028200	Active TSS	Stomach Smooth Muscle	stomach
25	chr13:52025200-52028200	Active TSS	HSMMtube	muscle
26	chr13:52025200-52028400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr13:52025200-52028600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr13:52025200-52028600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr13:52025200-52028600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr13:52025200-52028600	Active TSS	Aorta	Aorta
31	chr13:52025200-52028600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr13:52025200-52028600	Active TSS	Fetal Muscle Trunk	muscle
33	chr13:52025200-52028600	Active TSS	Lung	lung
34	chr13:52025200-52028600	Active TSS	A549	lung
35	chr13:52025200-52028800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:52025200-52028800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr13:52025200-52028800	Active TSS	Fetal Intestine Small	intestine
38	chr13:52025200-52028800	Active TSS	Fetal Thymus	thymus
39	chr13:52025200-52028800	Active TSS	Psoas Muscle	Psoas
40	chr13:52025200-52028800	Active TSS	NHDF-Ad	bronchial
41	chr13:52025400-52026000	Active TSS	Brain Germinal Matrix	brain
42	chr13:52025400-52026200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr13:52025400-52027800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr13:52025400-52028000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:52025400-52028000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:52025400-52028000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr13:52025400-52028000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr13:52025400-52028200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:52025400-52028200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr13:52025400-52028200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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