Variant report

Variant	rs9311490
Chromosome Location	chr3:53196361-53196362
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	IKZF1	chr3:53196309-53196651	GM12878	blood:	n/a	n/a
2	CHD2	chr3:53195384-53197613	GM12878	blood:	n/a	chr3:53196018-53196028
3	POU2F2	chr3:53196138-53197641	GM12878	blood:	n/a	chr3:53197328-53197340 chr3:53196280-53196292 chr3:53197160-53197172
4	MTA3	chr3:53196272-53196923	GM12878	blood:	n/a	n/a
5	BCLAF1	chr3:53196279-53197578	GM12878	blood:	n/a	n/a
6	SPI1	chr3:53196219-53196444	K562	blood:	n/a	n/a
7	EBF1	chr3:53195877-53198088	GM12878	blood:	n/a	chr3:53196035-53196044 chr3:53198051-53198064 chr3:53196997-53197006 chr3:53198053-53198062 chr3:53196034-53196045
8	POLR2A	chr3:53194482-53198512	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:53194588-53197470	GM19099	blood:	n/a	n/a
10	SIN3A	chr3:53196080-53197606	GM12878	blood:	n/a	n/a
11	ZEB1	chr3:53196202-53196636	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:53194575-53197885	GM18505	blood:	n/a	n/a
13	STAT5A	chr3:53196136-53198360	GM12878	blood:	n/a	chr3:53197773-53197781 chr3:53196376-53196388
14	MAZ	chr3:53195502-53197515	GM12878	blood:	n/a	chr3:53196435-53196445 chr3:53195952-53195962
15	POLR2A	chr3:53194684-53197963	GM12878	blood:	n/a	n/a
16	RELA	chr3:53196266-53197773	GM10847	blood:	n/a	n/a
17	SPI1	chr3:53196232-53196409	K562	blood:	n/a	n/a
18	SIN3A	chr3:53194552-53196395	H1-hESC	embryonic stem cell:	n/a	chr3:53194806-53194817
19	ELF1	chr3:53195906-53196618	GM12878	blood:	n/a	chr3:53196021-53196033
20	EP300	chr3:53195982-53196869	GM12878	blood:	n/a	n/a
21	SPI1	chr3:53196168-53196599	GM12878	blood:	n/a	n/a
22	ZNF263	chr3:53196269-53196981	HEK293-T-REx	kidney:	n/a	chr3:53196275-53196284
23	POLR2A	chr3:53194594-53197853	GM12878	blood:	n/a	n/a
24	SPI1	chr3:53196211-53196451	GM12878	blood:	n/a	n/a
25	EBF1	chr3:53195865-53196574	GM12878	blood:	n/a	chr3:53196035-53196044 chr3:53196034-53196045
26	MAX	chr3:53195682-53197734	NB4	blood:	n/a	chr3:53197434-53197444 chr3:53196435-53196445 chr3:53195952-53195962
27	POLR2A	chr3:53194615-53196516	GM15510	blood:	n/a	n/a
28	POLR2A	chr3:53194621-53197512	GM12878	blood:	n/a	n/a
29	MTA3	chr3:53195870-53198014	GM12878	blood:	n/a	n/a
30	EGR1	chr3:53196258-53196596	GM12878	blood:	n/a	chr3:53196431-53196442 chr3:53196430-53196444 chr3:53196429-53196444 chr3:53196431-53196445 chr3:53196287-53196297 chr3:53196430-53196443 chr3:53196432-53196442 chr3:53196430-53196443 chr3:53196430-53196443 chr3:53196426-53196448 chr3:53196430-53196443
31	POLR2A	chr3:53196131-53196367	K562	blood:	n/a	n/a
32	POLR2A	chr3:53194589-53196561	GM18951	blood:	n/a	n/a
33	BHLHE40	chr3:53195981-53197637	GM12878	blood:	n/a	n/a
34	BCLAF1	chr3:53196262-53197619	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:53194614-53197550	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:53194464-53197543	GM19193	blood:	n/a	n/a
37	POLR2A	chr3:53196171-53196410	K562	blood:	n/a	n/a
38	SPI1	chr3:53196156-53196674	HL-60	blood:	n/a	n/a
39	POLR2A	chr3:53194608-53197593	GM12878	blood:	n/a	n/a
40	SPI1	chr3:53196165-53196571	GM12891	blood:	n/a	n/a
41	POLR2A	chr3:53196345-53196865	GM12891	blood:	n/a	n/a
42	POLR2A	chr3:53196162-53196761	GM12891	blood:	n/a	n/a
43	EGR1	chr3:53196334-53196528	GM12878	blood:	n/a	chr3:53196431-53196442 chr3:53196430-53196444 chr3:53196429-53196444 chr3:53196431-53196445 chr3:53196430-53196443 chr3:53196432-53196442 chr3:53196430-53196443 chr3:53196430-53196443 chr3:53196426-53196448 chr3:53196430-53196443
44	POLR2A	chr3:53194552-53196890	HL-60	blood:	n/a	n/a
45	POLR2A	chr3:53195933-53198350	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:53194526-53197466	GM12892	blood:	n/a	n/a
47	ZMIZ1	chr3:53196313-53196477	K562	blood:	n/a	n/a
48	RUNX3	chr3:53196140-53197644	GM12878	blood:	n/a	n/a
49	ZBTB7A	chr3:53194511-53196526	ECC-1	luminal epithelium:	n/a	n/a
50	IRF4	chr3:53196139-53197646	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
2	chr3:53195653..53197299-chr3:53202368..53204305,2	K562	blood:
3	chr3:53163122..53165133-chr3:53195998..53198976,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10865978	1.00[AMR][1000 genomes]
rs10865979	1.00[AMR][1000 genomes]
rs2128709	1.00[AMR][1000 genomes]
rs55709737	1.00[AMR][1000 genomes]
rs6445567	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6445568	1.00[AMR][1000 genomes]
rs7622987	1.00[AMR][1000 genomes]

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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53194400-53196400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:53194400-53196400	Active TSS	Aorta	Aorta
3	chr3:53194400-53197000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:53194400-53197000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:53194400-53197000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:53194600-53196400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53194600-53196400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:53194600-53196400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:53194600-53196400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:53194600-53196400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:53194600-53196400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:53194600-53196400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:53194600-53196400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:53194600-53196400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:53194600-53196400	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:53194600-53196400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:53194600-53196400	Bivalent Enhancer	Fetal Brain Male	brain
18	chr3:53194600-53196400	Active TSS	Ovary	ovary
19	chr3:53194600-53196400	Active TSS	Psoas Muscle	Psoas
20	chr3:53194600-53196400	Active TSS	Right Ventricle	heart
21	chr3:53194600-53196400	Active TSS	HSMMtube	muscle
22	chr3:53194600-53196400	Active TSS	K562	blood
23	chr3:53194600-53196400	Active TSS	NHDF-Ad	bronchial
24	chr3:53194600-53196400	Active TSS	NHLF	lung
25	chr3:53194600-53196600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:53194600-53196600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:53194600-53196600	Active TSS	Brain Angular Gyrus	brain
28	chr3:53194600-53196600	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr3:53194600-53196600	Active TSS	Gastric	stomach
30	chr3:53194600-53196600	Active TSS	Left Ventricle	heart
31	chr3:53194600-53196600	Active TSS	Lung	lung
32	chr3:53194600-53196600	Active TSS	Small Intestine	intestine
33	chr3:53194600-53196800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:53194600-53197000	Active TSS	Brain Anterior Caudate	brain
35	chr3:53194600-53197200	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr3:53194600-53197200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:53194600-53197200	Active TSS	Fetal Kidney	kidney
38	chr3:53194600-53197400	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:53194600-53197400	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:53194800-53196400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr3:53194800-53196400	Active TSS	H1 Cell Line	embryonic stem cell
42	chr3:53194800-53196400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:53194800-53196400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:53194800-53196400	Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr3:53194800-53196400	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:53194800-53196400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:53194800-53196400	Active TSS	Liver	Liver
48	chr3:53194800-53196400	Active TSS	Colonic Mucosa	Colon
49	chr3:53194800-53196400	Active TSS	Duodenum Mucosa	Duodenum
50	chr3:53194800-53196400	Active TSS	Esophagus	oesophagus

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