Variant report

Variant	rs3756969
Chromosome Location	chr6:133134937-133134938
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	TCF12	chr6:133134391-133136145	A549	lung:	n/a	n/a
2	POLR2A	chr6:133133973-133142719	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:133134002-133136170	HCT-116	colon:	n/a	n/a
4	PAX5	chr6:133134681-133135040	GM12878	blood:	n/a	n/a
5	EGR1	chr6:133134759-133134965	GM12878	blood:	n/a	n/a
6	NR2F2	chr6:133134573-133136044	K562	blood:	n/a	n/a
7	TAF1	chr6:133134632-133136152	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:133134162-133138350	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:133133509-133142958	HepG2	liver:	n/a	n/a
10	NFIC	chr6:133134226-133134958	HepG2	liver:	n/a	n/a
11	E2F6	chr6:133134202-133134970	H1-hESC	embryonic stem cell:	n/a	chr6:133134503-133134510 chr6:133134605-133134614
12	STAT5A	chr6:133134219-133136486	GM12878	blood:	n/a	chr6:133134283-133134294 chr6:133134277-133134288 chr6:133135591-133135602 chr6:133134635-133134644 chr6:133134636-133134645
13	POLR2A	chr6:133134236-133136890	MCF-7	breast:	n/a	n/a
14	TBP	chr6:133133860-133135952	Hela-S3	cervix:	n/a	n/a
15	REST	chr6:133134150-133135002	HepG2	liver:	n/a	chr6:133134461-133134468
16	BATF	chr6:133134714-133135000	GM12878	blood:	n/a	n/a
17	MYC	chr6:133133521-133138056	K562	blood:	n/a	chr6:133134081-133134091 chr6:133135767-133135777
18	HDAC2	chr6:133134394-133134960	HepG2	liver:	n/a	chr6:133134521-133134535
19	POLR2A	chr6:133134007-133138262	GM15510	blood:	n/a	n/a
20	POLR2A	chr6:133134121-133142902	PFSK-1	brain:	n/a	n/a
21	HA-E2F1	chr6:133134284-133136173	MCF-7	breast:	n/a	chr6:133134503-133134510 chr6:133134605-133134614 chr6:133135649-133135658
22	YY1	chr6:133134400-133135914	H1-hESC	embryonic stem cell:	n/a	chr6:133135767-133135778
23	PAX5	chr6:133134665-133135043	GM12878	blood:	n/a	n/a
24	MTA3	chr6:133133767-133137277	GM12878	blood:	n/a	n/a
25	RELA	chr6:133134071-133135940	GM19193	blood:	n/a	n/a
26	POLR2A	chr6:133134120-133142624	GM18505	blood:	n/a	n/a
27	TEAD4	chr6:133134159-133135002	K562	blood:	n/a	n/a
28	TBL1XR1	chr6:133134061-133136057	GM12878	blood:	n/a	n/a
29	PAX5	chr6:133134697-133135132	GM12891	blood:	n/a	n/a
30	POLR2A	chr6:133134787-133136856	PANC-1	pancreas:	n/a	n/a
31	RELA	chr6:133133625-133136264	GM10847	blood:	n/a	n/a
32	YY1	chr6:133134386-133134966	K562	blood:	n/a	n/a
33	TAF7	chr6:133134418-133138128	H1-hESC	embryonic stem cell:	n/a	n/a
34	BHLHE40	chr6:133133833-133136004	GM12878	blood:	n/a	chr6:133134469-133134478 chr6:133134469-133134478
35	POLR2A	chr6:133133442-133144695	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr6:133133522-133142994	GM12891	blood:	n/a	n/a
37	POLR2A	chr6:133134246-133136628	K562	blood:	n/a	n/a
38	IRF4	chr6:133133951-133135053	GM12878	blood:	n/a	chr6:133134281-133134295 chr6:133134277-133134298
39	MXI1	chr6:133133461-133135102	IMR90	lung:	n/a	n/a
40	RCOR1	chr6:133134415-133135994	HepG2	liver:	n/a	n/a
41	RFX5	chr6:133134236-133135895	Hela-S3	cervix:	n/a	n/a
42	SPI1	chr6:133134438-133135234	GM12878	blood:	n/a	n/a
43	EGR1	chr6:133134759-133134973	K562	blood:	n/a	n/a
44	POLR2A	chr6:133134287-133134986	HCT-116	colon:	n/a	n/a
45	RELA	chr6:133133917-133136548	GM12891	blood:	n/a	n/a
46	MAX	chr6:133134228-133136485	HCT-116	colon:	n/a	chr6:133135767-133135777
47	POLR2A	chr6:133133648-133142538	K562	blood:	n/a	n/a
48	MYC	chr6:133134159-133136405	NB4	blood:	n/a	chr6:133135767-133135777
49	IRF1	chr6:133133384-133137081	K562	blood:	n/a	chr6:133134277-133134291 chr6:133134280-133134294 chr6:133135591-133135605 chr6:133135587-133135601 chr6:133134911-133134922 chr6:133134281-133134294 chr6:133134277-133134287 chr6:133134278-133134289 chr6:133134276-133134288 chr6:133134276-133134293 chr6:133135464-133135478 chr6:133134283-133134294 chr6:133134281-133134294 chr6:133134283-133134293 chr6:133135589-133135602 chr6:133135583-133135603 chr6:133134284-133134295 chr6:133134275-133134288 chr6:133134283-133134297 chr6:133134279-133134293 chr6:133134275-133134289 chr6:133135591-133135601 chr6:133134277-133134288 chr6:133134276-133134289 chr6:133135589-133135602 chr6:133134276-133134290 chr6:133135589-133135603 chr6:133134277-133134298 chr6:133134281-133134294 chr6:133134275-133134295 chr6:133134281-133134294 chr6:133135588-133135602 chr6:133134281-133134295 chr6:133134605-133134614
50	RCOR1	chr6:133134420-133136183	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:133084942..133087324-chr6:133134860..133137280,2	MCF-7	breast:
2	chr6:133133722..133135487-chr6:133500551..133504315,3	K562	blood:
3	chr14:69259781..69261291-chr6:133134489..133136848,2	MCF-7	breast:
4	chr6:133132887..133135811-chr6:134273188..134277510,5	K562	blood:
5	chr12:46121390..46121921-chr6:133134920..133135826,2	Hela-S3	cervix:
6	chr6:132832429..132834669-chr6:133134284..133137002,3	K562	blood:
7	chr6:132965299..132967214-chr6:133134332..133136020,2	K562	blood:
8	chr1:853806..855355-chr6:133134480..133137289,2	MCF-7	breast:
9	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
10	chr6:133118544..133124606-chr6:133132137..133138834,13	MCF-7	breast:
11	chr6:133134320..133137127-chr6:136569335..136571574,2	K562	blood:
12	chr6:132833194..132835178-chr6:133134140..133136704,2	MCF-7	breast:
13	chr6:132994919..132997703-chr6:133134162..133135954,3	MCF-7	breast:
14	chr6:133117688..133126502-chr6:133133829..133139054,19	MCF-7	breast:

Variant related genes	Relation type
SNORD100	TF binding region
SNORA33	TF binding region
SNORD101	TF binding region
RPS12	TF binding region
ENSG00000271488	Chromatin interaction
ENSG00000146409	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000112303	Chromatin interaction
ENSG00000218194	Chromatin interaction
ENSG00000146410	Chromatin interaction
ENSG00000079950	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000146399	Chromatin interaction
ENSG00000028839	Chromatin interaction
ENSG00000223764	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11154696	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12202302	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983607	0.88[EUR][1000 genomes]
rs3778174	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6569855	0.87[ASN][1000 genomes]
rs6921262	0.87[ASN][1000 genomes]
rs6926466	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927761	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs761125	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9321378	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9375921	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9389035	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9493451	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9493459	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133133400-133135800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:133133400-133136000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:133133400-133136000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:133133400-133136200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:133133400-133136200	Active TSS	NHDF-Ad	bronchial
6	chr6:133133400-133136400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:133133600-133135000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:133133600-133135200	Active TSS	Right Atrium	heart
9	chr6:133133600-133135400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:133133600-133135400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:133133600-133135400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:133133600-133135400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:133133600-133136000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:133133600-133136000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:133133600-133136000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:133133600-133136000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:133133600-133136000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:133133600-133136000	Active TSS	Fetal Lung	lung
19	chr6:133133600-133136200	Active TSS	Brain Substantia Nigra	brain
20	chr6:133133600-133136400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr6:133133600-133136400	Active TSS	Brain Angular Gyrus	brain
22	chr6:133133600-133136400	Active TSS	Brain Anterior Caudate	brain
23	chr6:133133600-133136600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:133133600-133136600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:133133600-133136800	Active TSS	Brain Cingulate Gyrus	brain
26	chr6:133133600-133137000	Active TSS	Aorta	Aorta
27	chr6:133133600-133137000	Active TSS	Fetal Intestine Small	intestine
28	chr6:133133600-133137000	Active TSS	Ovary	ovary
29	chr6:133133600-133137000	Active TSS	Thymus	Thymus
30	chr6:133133600-133137200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:133133600-133137200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:133133600-133137200	Active TSS	Colonic Mucosa	Colon
33	chr6:133133800-133135800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:133133800-133136000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr6:133133800-133136200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:133133800-133136200	Active TSS	Stomach Smooth Muscle	stomach
37	chr6:133133800-133136400	Active TSS	Fetal Thymus	thymus
38	chr6:133133800-133136600	Active TSS	Colon Smooth Muscle	Colon
39	chr6:133133800-133136600	Active TSS	Small Intestine	intestine
40	chr6:133133800-133136800	Active TSS	Fetal Muscle Trunk	muscle
41	chr6:133133800-133136800	Active TSS	Placenta	Placenta
42	chr6:133133800-133136800	Active TSS	Fetal Stomach	stomach
43	chr6:133133800-133137000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:133133800-133137000	Active TSS	Fetal Intestine Large	intestine
45	chr6:133133800-133137000	Active TSS	Right Ventricle	heart
46	chr6:133133800-133137000	Active TSS	Sigmoid Colon	Sigmoid Colon
47	chr6:133133800-133137000	Active TSS	Stomach Mucosa	stomach
48	chr6:133133800-133137200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:133134000-133135400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr6:133134000-133136000	Active TSS	HUES48 Cell Line	embryonic stem cell

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