Variant report

Variant	rs492404
Chromosome Location	chr13:30509774-30509775
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	PML	chr13:30509566-30510290	GM12878	blood:	n/a	n/a
2	EP300	chr13:30509614-30510144	GM12878	blood:	n/a	chr13:30509845-30509858
3	TCF3	chr13:30509663-30510110	GM12878	blood:	n/a	chr13:30509889-30509904 chr13:30509698-30509711 chr13:30509892-30509901
4	NFATC1	chr13:30509596-30510183	GM12878	blood:	n/a	n/a
5	MTA3	chr13:30509593-30510078	GM12878	blood:	n/a	n/a
6	BCL11A	chr13:30509708-30510029	GM12878	blood:	n/a	n/a
7	SP1	chr13:30509670-30510166	GM12878	blood:	n/a	n/a
8	IRF4	chr13:30509632-30510097	GM12878	blood:	n/a	n/a
9	STAT5A	chr13:30509605-30510200	GM12878	blood:	n/a	n/a
10	MEF2A	chr13:30509585-30510258	GM12878	blood:	n/a	chr13:30510067-30510088 chr13:30510071-30510086 chr13:30510074-30510083 chr13:30510067-30510088 chr13:30510071-30510087 chr13:30510067-30510088 chr13:30510072-30510087 chr13:30510072-30510086 chr13:30510073-30510084
11	BCL11A	chr13:30509639-30510100	GM12878	blood:	n/a	n/a
12	RCOR1	chr13:30509766-30510358	GM12878	blood:	n/a	n/a
13	ATF2	chr13:30509673-30510145	GM12878	blood:	n/a	n/a
14	EBF1	chr13:30509645-30510140	GM12878	blood:	n/a	n/a
15	BATF	chr13:30509685-30510043	GM12878	blood:	n/a	n/a
16	EP300	chr13:30509582-30510182	GM12878	blood:	n/a	chr13:30509845-30509858
17	FOXM1	chr13:30509511-30510274	GM12878	blood:	n/a	n/a
18	RUNX3	chr13:30509501-30510184	GM12878	blood:	n/a	n/a
19	BCL3	chr13:30509682-30510023	GM12878	blood:	n/a	n/a
20	BCLAF1	chr13:30509578-30510246	GM12878	blood:	n/a	n/a
21	MEF2C	chr13:30509715-30510298	GM12878	blood:	n/a	chr13:30510067-30510088 chr13:30510071-30510086 chr13:30510074-30510083 chr13:30510067-30510088 chr13:30510071-30510087 chr13:30510067-30510088 chr13:30510072-30510087 chr13:30510072-30510086 chr13:30510073-30510084
22	PAX5	chr13:30509762-30510031	GM12878	blood:	n/a	n/a
23	SP1	chr13:30509699-30510052	GM12878	blood:	n/a	n/a
24	PAX5	chr13:30509774-30510035	GM12878	blood:	n/a	n/a
25	CHD2	chr13:30509662-30510348	GM12878	blood:	n/a	n/a
26	STAT5A	chr13:30509704-30510035	GM12878	blood:	n/a	n/a
27	MEF2A	chr13:30509685-30510181	GM12878	blood:	n/a	chr13:30510067-30510088 chr13:30510071-30510086 chr13:30510074-30510083 chr13:30510067-30510088 chr13:30510071-30510087 chr13:30510067-30510088 chr13:30510072-30510087 chr13:30510072-30510086 chr13:30510073-30510084
28	SPI1	chr13:30509665-30510491	HL-60	blood:	n/a	n/a
29	TBL1XR1	chr13:30509559-30510222	GM12878	blood:	n/a	n/a
30	EBF1	chr13:30509630-30510032	GM12878	blood:	n/a	n/a
31	NFIC	chr13:30509560-30510208	GM12878	blood:	n/a	n/a
32	MAZ	chr13:30509696-30510328	GM12878	blood:	n/a	n/a
33	EBF1	chr13:30509430-30510095	GM12878	blood:	n/a	n/a
34	EP300	chr13:30509656-30510164	GM12878	blood:	n/a	chr13:30509845-30509858
35	TCF3	chr13:30509620-30510558	GM12878	blood:	n/a	chr13:30509889-30509904 chr13:30509698-30509711 chr13:30509892-30509901
36	TCF12	chr13:30509704-30510166	GM12878	blood:	n/a	n/a
37	MTA3	chr13:30509549-30510491	GM12878	blood:	n/a	n/a
38	ATF2	chr13:30509557-30510249	GM12878	blood:	n/a	n/a
39	YY1	chr13:30509612-30510090	GM12878	blood:	n/a	n/a
40	NFIC	chr13:30509604-30510200	GM12878	blood:	n/a	n/a
41	ETS1	chr13:30509728-30510089	GM12878	blood:	n/a	chr13:30509993-30510004
42	ZNF143	chr13:30509672-30510087	GM12878	blood:	n/a	n/a
43	TCF12	chr13:30509667-30510131	GM12878	blood:	n/a	n/a
44	PAX5	chr13:30509659-30510087	GM12878	blood:	n/a	n/a
45	WRNIP1	chr13:30509713-30510075	GM12878	blood:	n/a	n/a
46	IRF4	chr13:30509583-30510165	GM12878	blood:	n/a	n/a
47	FOXM1	chr13:30509632-30510232	GM12878	blood:	n/a	n/a
48	BHLHE40	chr13:30509657-30510198	GM12878	blood:	n/a	n/a
49	POLR2A	chr13:30509722-30509845	H1-hESC	embryonic stem cell:	n/a	n/a
50	RUNX3	chr13:30509478-30510190	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30508008..30510755-chr13:30510923..30512750,2	MCF-7	breast:

Variant related genes	Relation type
LINC00544	TF binding region
ENSG00000122043	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3847988	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs598473	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61947282	0.88[EUR][1000 genomes]
rs61947284	0.88[EUR][1000 genomes]
rs61947285	0.88[EUR][1000 genomes]
rs660017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7323424	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs927734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9508593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30498800-30513200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:30499000-30510000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr13:30508000-30510000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:30508000-30510000	Enhancers	Thymus	Thymus
5	chr13:30508200-30509800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr13:30508200-30510000	Enhancers	Primary T cells from cord blood	blood
7	chr13:30508200-30510000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:30508200-30510000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr13:30508400-30509800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr13:30508400-30509800	Enhancers	Fetal Brain Female	brain
11	chr13:30508400-30510000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr13:30508400-30510000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr13:30508400-30510000	Enhancers	Fetal Thymus	thymus
14	chr13:30508600-30509800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr13:30508600-30510400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:30508800-30509800	Enhancers	Brain Cingulate Gyrus	brain
17	chr13:30508800-30510600	Enhancers	Fetal Brain Male	brain
18	chr13:30509000-30509800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr13:30509000-30510800	Enhancers	Stomach Mucosa	stomach
20	chr13:30509000-30512600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:30509200-30510000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr13:30509200-30510000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr13:30509200-30510200	Enhancers	Duodenum Mucosa	Duodenum
24	chr13:30509200-30510400	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr13:30509200-30510600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr13:30509200-30511000	Enhancers	Primary B cells from peripheral blood	blood
27	chr13:30509400-30509800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr13:30509400-30509800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr13:30509400-30509800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:30509400-30509800	Bivalent Enhancer	Placenta	Placenta
31	chr13:30509400-30510000	Enhancers	Primary B cells from cord blood	blood
32	chr13:30509400-30510000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:30509400-30510000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:30509400-30510000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:30509400-30510200	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr13:30509400-30510200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr13:30509400-30510400	Enhancers	H1 Cell Line	embryonic stem cell
38	chr13:30509400-30510400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr13:30509400-30510600	Enhancers	Fetal Intestine Large	intestine
40	chr13:30509400-30510600	Flanking Active TSS	GM12878-XiMat	blood
41	chr13:30509400-30510800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:30509400-30511600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:30509400-30511600	Enhancers	Liver	Liver
44	chr13:30509400-30512800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr13:30509600-30510000	Weak transcription	Brain Anterior Caudate	brain
46	chr13:30509600-30510000	Enhancers	Right Atrium	heart
47	chr13:30509600-30510400	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr13:30509600-30510600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:30509600-30510800	Enhancers	Brain Hippocampus Middle	brain
50	chr13:30509600-30510800	Enhancers	Fetal Intestine Small	intestine

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