Variant report

Variant	rs564258534
Chromosome Location	chr13:52025411-52025412
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr13:52025211-52025876	K562	blood:	n/a	n/a
2	USF2	chr13:52025273-52025701	K562	blood:	n/a	chr13:52025633-52025649
3	TAL1	chr13:52025280-52027330	K562	blood:	n/a	n/a
4	POLR2A	chr13:52023042-52028956	GM12878	blood:	n/a	n/a
5	CHD1	chr13:52024742-52028646	IMR90	lung:	n/a	n/a
6	CHD1	chr13:52025386-52028410	GM12878	blood:	n/a	n/a
7	POLR2A	chr13:52025258-52028416	K562	blood:	n/a	n/a
8	POLR2A	chr13:52025304-52026371	PBDE	blood:	n/a	n/a
9	POLR2A	chr13:52025371-52028505	GM18951	blood:	n/a	n/a
10	REST	chr13:52025376-52028611	H1-neurons	neurons:	n/a	chr13:52027338-52027356 chr13:52025635-52025644 chr13:52025993-52026006
11	POLR2A	chr13:52024109-52028486	GM18505	blood:	n/a	n/a
12	POLR2A	chr13:52025341-52025485	GM12878	blood:	n/a	n/a
13	POLR2A	chr13:52025194-52025831	GM12891	blood:	n/a	n/a
14	POLR2A	chr13:52023653-52028418	HepG2	liver:	n/a	n/a
15	TBP	chr13:52025349-52026368	K562	blood:	n/a	n/a
16	MTA3	chr13:52025208-52028795	GM12878	blood:	n/a	n/a
17	MAZ	chr13:52025242-52028542	IMR90	lung:	n/a	chr13:52027243-52027256 chr13:52027244-52027255 chr13:52027245-52027254 chr13:52027244-52027255 chr13:52027240-52027259
18	POLR2A	chr13:52025284-52028366	HepG2	liver:	n/a	n/a
19	IRF1	chr13:52025252-52026232	K562	blood:	n/a	chr13:52025338-52025348 chr13:52025396-52025410 chr13:52025397-52025409 chr13:52025334-52025348
20	POLR2A	chr13:52024356-52028620	GM12878	blood:	n/a	n/a
21	POLR2A	chr13:52025303-52028702	GM12892	blood:	n/a	n/a
22	POLR2A	chr13:52024960-52027314	K562	blood:	n/a	n/a
23	POLR2A	chr13:52025388-52028613	Raji	blood:	n/a	n/a
24	STAT5A	chr13:52025163-52025888	GM12878	blood:	n/a	n/a
25	POLR2A	chr13:52025381-52028561	K562	blood:	n/a	n/a
26	POLR2A	chr13:52025232-52027326	GM12891	blood:	n/a	n/a
27	ARID3A	chr13:52025285-52025435	K562	blood:	n/a	n/a
28	MAZ	chr13:52025304-52028450	GM12878	blood:	n/a	chr13:52027243-52027256 chr13:52027244-52027255 chr13:52027245-52027254 chr13:52027244-52027255 chr13:52027240-52027259
29	POLR2A	chr13:52025393-52028357	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr13:52024349-52028618	GM12878	blood:	n/a	n/a
31	POLR2A	chr13:52025287-52028853	GM19099	blood:	n/a	n/a
32	PML	chr13:52025293-52028928	GM12878	blood:	n/a	n/a
33	SPI1	chr13:52025333-52026265	HL-60	blood:	n/a	chr13:52025492-52025499
34	POLR2A	chr13:52025199-52028610	GM12892	blood:	n/a	n/a
35	ARID3A	chr13:52025323-52025870	HepG2	liver:	n/a	n/a
36	POLR2A	chr13:52025146-52028380	K562	blood:	n/a	n/a
37	CHD2	chr13:52025411-52028351	GM12878	blood:	n/a	n/a
38	YY1	chr13:52025354-52026301	SK-N-SH	brain:	n/a	chr13:52025841-52025849 chr13:52025751-52025765 chr13:52025837-52025849 chr13:52025835-52025855 chr13:52025836-52025855
39	POLR2A	chr13:52025131-52028505	H1-hESC	embryonic stem cell:	n/a	n/a
40	RELA	chr13:52025369-52028476	GM12891	blood:	n/a	n/a
41	TBP	chr13:52025358-52025819	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr13:52025282-52028198	HUVEC	blood vessel:	n/a	n/a
43	WRNIP1	chr13:52025344-52025726	GM12878	blood:	n/a	n/a
44	POLR2A	chr13:52025187-52026383	SK-N-MC	brain:	n/a	n/a
45	TBL1XR1	chr13:52025364-52025552	K562	blood:	n/a	n/a
46	POLR2A	chr13:52025346-52025509	GM12878	blood:	n/a	n/a
47	POLR2A	chr13:52025359-52025459	MCF-7	breast:	n/a	n/a
48	POLR2A	chr13:52025331-52028520	GM12891	blood:	n/a	n/a
49	POLR2A	chr13:52025339-52028460	GM19193	blood:	n/a	n/a
50	MYC	chr13:52025189-52025831	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52022728..52028464-chr13:52376436..52381467,17	K562	blood:
2	chr13:52023047..52029598-chr13:52376243..52380914,21	K562	blood:
3	chr13:52022475..52029228-chr13:52156654..52162250,29	K562	blood:
4	chr13:51933288..51938259-chr13:52024808..52026901,4	K562	blood:
5	chr13:52022170..52025698-chr13:52211557..52214174,3	MCF-7	breast:
6	chr13:52025248..52027565-chr13:52113097..52117557,5	K562	blood:
7	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:
8	chr13:52025241..52027687-chr13:52171016..52174536,3	MCF-7	breast:
9	chr13:52024267..52031024-chr13:52038927..52044194,9	MCF-7	breast:
10	chr13:52024232..52029374-chr13:52366504..52381003,28	MCF-7	breast:
11	chr13:52023587..52026212-chr20:45985508..45987866,2	MCF-7	breast:
12	chr13:52022285..52029211-chr13:52148229..52167071,88	MCF-7	breast:
13	chr13:51994030..51996463-chr13:52024763..52027853,3	MCF-7	breast:
14	chr13:52025027..52027980-chr2:128047526..128049328,2	MCF-7	breast:
15	chr13:52024284..52029908-chr13:52069886..52073128,6	K562	blood:
16	chr13:52024964..52027210-chr3:57581929..57583601,2	MCF-7	breast:
17	chr13:52025248..52026911-chr13:52113097..52115719,3	K562	blood:
18	chr13:52025134..52027888-chr13:53029090..53030597,2	MCF-7	breast:
19	chr13:52023038..52025684-chr13:52169375..52171570,2	K562	blood:
20	chr13:52022042..52032158-chr13:52153162..52160287,46	K562	blood:
21	chr13:52022276..52028052-chr13:52350866..52359408,15	MCF-7	breast:
22	chr13:52023374..52025771-chr13:52171326..52173571,2	MCF-7	breast:
23	chr13:52024743..52028940-chr13:52112359..52118516,11	MCF-7	breast:
24	chr13:52025316..52028305-chr18:3447499..3449683,2	MCF-7	breast:
25	chr13:52024180..52026043-chr13:52139073..52141757,2	K562	blood:
26	chr13:52025411..52028275-chr17:56707657..56710350,3	MCF-7	breast:
27	chr13:52023359..52028039-chr13:52370142..52379804,19	MCF-7	breast:
28	chr13:52015950..52029988-chr13:52150583..52166755,85	MCF-7	breast:

No data

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

Extended variants
information (count: 1 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51995600-52025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:52023800-52025600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:52024200-52025600	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr13:52024200-52025600	Enhancers	Fetal Heart	heart
5	chr13:52024400-52028200	Active TSS	Thymus	Thymus
6	chr13:52024600-52025600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr13:52024600-52025600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr13:52024600-52025600	Transcr. at gene 5' and 3'	HepG2	liver
9	chr13:52024600-52025600	Transcr. at gene 5' and 3'	Osteobl	bone
10	chr13:52024800-52025600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr13:52024800-52025600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr13:52024800-52025800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:52024800-52026600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:52024800-52027200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:52025000-52025600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:52025000-52025600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
17	chr13:52025000-52025600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
18	chr13:52025000-52025600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:52025000-52025600	Flanking Active TSS	Fetal Lung	lung
20	chr13:52025000-52025600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr13:52025000-52025600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr13:52025000-52025800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr13:52025000-52025800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr13:52025000-52025800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr13:52025000-52025800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:52025000-52025800	Active TSS	Right Atrium	heart
27	chr13:52025000-52028000	Active TSS	Hela-S3	cervix
28	chr13:52025000-52028000	Active TSS	HMEC	breast
29	chr13:52025000-52028200	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr13:52025000-52028200	Active TSS	Primary T cells fromperipheralblood	blood
31	chr13:52025000-52028200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr13:52025000-52028600	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr13:52025000-52028600	Active TSS	Right Ventricle	heart
34	chr13:52025000-52028800	Active TSS	Fetal Muscle Leg	muscle
35	chr13:52025000-52028800	Active TSS	K562	blood
36	chr13:52025000-52029000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:52025000-52029000	Active TSS	GM12878-XiMat	blood
38	chr13:52025200-52025600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr13:52025200-52025600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr13:52025200-52025600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:52025200-52025600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:52025200-52025600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr13:52025200-52025600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr13:52025200-52025600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr13:52025200-52025600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr13:52025200-52025600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr13:52025200-52025600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr13:52025200-52025600	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr13:52025200-52025600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr13:52025200-52025600	Flanking Active TSS	Fetal Kidney	kidney

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