Variant report

Variant	rs968588
Chromosome Location	chr3:52489564-52489565
allele	A/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	BACH1	chr3:52489268-52489596	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF2	chr3:52489309-52489564	H1-hESC	embryonic stem cell:	n/a	n/a
3	ELF1	chr3:52489084-52490154	GM12878	blood:	n/a	chr3:52489419-52489428 chr3:52489635-52489647
4	USF1	chr3:52489284-52489566	K562	blood:	n/a	n/a
5	ATF3	chr3:52489558-52489760	K562	blood:	n/a	chr3:52489600-52489609
6	YY1	chr3:52489305-52489816	HCT-116	colon:	n/a	chr3:52489600-52489609 chr3:52489526-52489546 chr3:52489628-52489642 chr3:52489631-52489645
7	BHLHE40	chr3:52489199-52489621	A549	lung:	n/a	chr3:52489598-52489614 chr3:52489601-52489617
8	MYC	chr3:52489246-52489715	K562	blood:	n/a	n/a
9	POLR2A	chr3:52489345-52489844	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:52489194-52489912	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr3:52489030-52490008	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:52489455-52489845	U87	brain:	n/a	n/a
13	MAX	chr3:52489231-52489910	H1-hESC	embryonic stem cell:	n/a	chr3:52489875-52489885
14	POLR2A	chr3:52489357-52489850	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:52489106-52490017	U87	brain:	n/a	n/a
16	YY1	chr3:52489392-52489715	HCT-116	colon:	n/a	chr3:52489600-52489609 chr3:52489526-52489546 chr3:52489628-52489642 chr3:52489631-52489645
17	YY1	chr3:52489232-52489911	SK-N-SH_RA	brain:	n/a	chr3:52489600-52489609 chr3:52489526-52489546 chr3:52489628-52489642 chr3:52489631-52489645
18	POLR2A	chr3:52489197-52489871	GM12892	blood:	n/a	n/a
19	PBX3	chr3:52489092-52489871	SK-N-SH	brain:	n/a	chr3:52489483-52489492
20	RELA	chr3:52489181-52489812	GM15510	blood:	n/a	n/a
21	TAF1	chr3:52489508-52489777	SK-N-SH	brain:	n/a	n/a
22	CREB1	chr3:52489291-52489854	K562	blood:	n/a	n/a
23	TAF1	chr3:52489193-52489979	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr3:52489333-52489800	A549	lung:	n/a	n/a
25	POLR2A	chr3:52489222-52489860	NB4	blood:	n/a	n/a
26	TAF1	chr3:52489193-52490991	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr3:52489216-52489866	GM15510	blood:	n/a	n/a
28	POLR2A	chr3:52489234-52489864	HEK293	kidney:	n/a	n/a
29	TAF1	chr3:52489349-52489871	K562	blood:	n/a	n/a
30	POLR2A	chr3:52489563-52489797	SK-N-SH	brain:	n/a	n/a
31	ZBTB7A	chr3:52489307-52490753	ECC-1	luminal epithelium:	n/a	chr3:52489757-52489766
32	EGR1	chr3:52489332-52489695	H1-hESC	embryonic stem cell:	n/a	chr3:52489598-52489612 chr3:52489553-52489567
33	YY1	chr3:52489293-52489874	H1-hESC	embryonic stem cell:	n/a	chr3:52489600-52489609 chr3:52489526-52489546 chr3:52489628-52489642 chr3:52489631-52489645
34	JUND	chr3:52489208-52489788	K562	blood:	n/a	n/a
35	MAX	chr3:52489015-52489966	A549	lung:	n/a	chr3:52489875-52489885
36	MAX	chr3:52489255-52489612	A549	lung:	n/a	n/a
37	EGR1	chr3:52489367-52489846	K562	blood:	n/a	chr3:52489777-52489786 chr3:52489753-52489766 chr3:52489598-52489612 chr3:52489553-52489567 chr3:52489774-52489787
38	MAZ	chr3:52489328-52489792	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:52489426-52489844	A549	lung:	n/a	n/a
40	POLR2A	chr3:52489253-52489925	HCT-116	colon:	n/a	n/a
41	MYC	chr3:52489263-52489818	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr3:52489252-52489833	K562	blood:	n/a	chr3:52489758-52489767 chr3:52489600-52489609
43	CEBPB	chr3:52489151-52489635	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr3:52489142-52489851	GM12891	blood:	n/a	n/a
45	RFX5	chr3:52489226-52489729	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:52489213-52489913	MCF-7	breast:	n/a	n/a
47	HEY1	chr3:52489564-52489794	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:52489062-52490073	K562	blood:	n/a	n/a
49	CEBPD	chr3:52489192-52489747	K562	blood:	n/a	n/a
50	TBL1XR1	chr3:52489319-52489853	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
2	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
3	chr3:52489123..52491255-chr3:52558992..52560564,2	MCF-7	breast:
4	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:
5	chr3:52488362..52490407-chr3:52528579..52530282,2	K562	blood:
6	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:
7	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
8	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
9	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
10	chr3:52485198..52486814-chr3:52487911..52490387,2	K562	blood:
11	chr3:52447983..52449593-chr3:52487471..52490265,2	K562	blood:
12	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
13	chr3:52444497..52446102-chr3:52488760..52490756,2	K562	blood:
14	chr3:52481830..52487806-chr3:52487911..52490298,8	K562	blood:
15	chr3:52321768..52324071-chr3:52488633..52490328,2	K562	blood:

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000010318	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000163938	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1035002	0.81[AMR][1000 genomes]
rs13074649	0.85[AMR][1000 genomes]
rs2215466	0.85[AMR][1000 genomes]
rs3774409	0.85[AMR][1000 genomes]
rs4687541	0.85[AMR][1000 genomes]
rs4687614	0.85[AMR][1000 genomes]
rs6771558	0.85[AMR][1000 genomes]
rs9850471	0.85[AMR][1000 genomes]
rs9855470	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 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	chr3:52481200-52490000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52488600-52490600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:52488800-52489600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:52488800-52491800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:52489000-52489600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:52489000-52489600	Flanking Active TSS	HMEC	breast
7	chr3:52489000-52490200	Active TSS	Esophagus	oesophagus
8	chr3:52489000-52490800	Active TSS	Aorta	Aorta
9	chr3:52489000-52490800	Active TSS	Fetal Kidney	kidney
10	chr3:52489000-52490800	Active TSS	Ovary	ovary
11	chr3:52489000-52491200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:52489200-52490000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
13	chr3:52489200-52490200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:52489200-52490200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:52489200-52490200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:52489200-52490200	Active TSS	Colonic Mucosa	Colon
17	chr3:52489200-52490200	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr3:52489200-52490200	Active TSS	Small Intestine	intestine
19	chr3:52489200-52490200	Active TSS	Thymus	Thymus
20	chr3:52489200-52490200	Active TSS	Spleen	Spleen
21	chr3:52489200-52490400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:52489200-52490400	Active TSS	Brain Hippocampus Middle	brain
23	chr3:52489200-52490600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr3:52489200-52490600	Active TSS	Gastric	stomach
25	chr3:52489200-52490600	Active TSS	Left Ventricle	heart
26	chr3:52489200-52490600	Active TSS	Lung	lung
27	chr3:52489200-52490600	Active TSS	Psoas Muscle	Psoas
28	chr3:52489200-52490600	Active TSS	A549	lung
29	chr3:52489200-52490800	Active TSS	Right Atrium	heart
30	chr3:52489200-52491000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:52489400-52489600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:52489400-52489600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:52489400-52489600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:52489400-52489600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:52489400-52489800	Active TSS	Primary B cells from cord blood	blood
36	chr3:52489400-52489800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:52489400-52489800	Active TSS	HepG2	liver
38	chr3:52489400-52490000	Active TSS	Primary monocytes fromperipheralblood	blood
39	chr3:52489400-52490000	Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:52489400-52490000	Active TSS	Primary B cells from peripheral blood	blood
41	chr3:52489400-52490000	Active TSS	Primary T cells fromperipheralblood	blood
42	chr3:52489400-52490000	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr3:52489400-52490000	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr3:52489400-52490000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:52489400-52490000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:52489400-52490000	Active TSS	Adipose Nuclei	Adipose
47	chr3:52489400-52490000	Weak transcription	Fetal Brain Male	brain
48	chr3:52489400-52490000	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:52489400-52490000	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:52489400-52490000	Active TSS	Skeletal Muscle Female	skeletal muscle

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