Variant report

Variant	rs5745580
Chromosome Location	chr6:33546701-33546702
allele	A/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	CHD1	chr6:33546060-33546862	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:33544423-33548349	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr6:33545992-33546727	GM12878	blood:	n/a	n/a
4	CTCF	chr6:33546600-33546750	HRE	kidney:	n/a	chr6:33546607-33546620
5	CTCF	chr6:33546700-33546850	GM12868	blood:	n/a	n/a
6	MTA3	chr6:33546095-33546982	GM12878	blood:	n/a	n/a
7	WRNIP1	chr6:33546699-33546848	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:33546021-33546903	GM12878	blood:	n/a	n/a
9	EGR1	chr6:33546459-33546730	GM12878	blood:	n/a	chr6:33546662-33546669 chr6:33546610-33546625 chr6:33546612-33546626 chr6:33546653-33546666
10	CTCF	chr6:33546700-33546850	GM12866	blood:	n/a	n/a
11	CHD2	chr6:33545927-33546813	GM12878	blood:	n/a	n/a
12	STAT2	chr6:33546251-33546710	K562	blood:	n/a	chr6:33546523-33546538 chr6:33546647-33546659 chr6:33546520-33546531 chr6:33546612-33546624
13	POLR2A	chr6:33546216-33546968	GM12892	blood:	n/a	n/a
14	CTCF	chr6:33546560-33546710	GM12864	blood:	n/a	chr6:33546607-33546620
15	CTCF	chr6:33546640-33546790	GM12872	blood:	n/a	n/a
16	MAZ	chr6:33546402-33546735	K562	blood:	n/a	chr6:33546610-33546620
17	POLR2A	chr6:33546173-33547098	GM12878	blood:	n/a	n/a
18	MAZ	chr6:33546039-33546833	GM12878	blood:	n/a	chr6:33546610-33546620
19	IRF4	chr6:33546185-33546706	GM12878	blood:	n/a	chr6:33546515-33546536 chr6:33546519-33546533
20	CTCF	chr6:33546700-33546850	K562	blood:	n/a	n/a
21	ZBTB7A	chr6:33546370-33546837	K562	blood:	n/a	n/a
22	RUNX3	chr6:33545970-33546862	GM12878	blood:	n/a	n/a
23	CTCF	chr6:33546499-33546703	GM12891	blood:	n/a	chr6:33546607-33546620
24	CTCF	chr6:33546640-33546890	GM12867	blood:	n/a	n/a
25	SP1	chr6:33546303-33546753	GM12878	blood:	n/a	chr6:33546320-33546333 chr6:33546652-33546661 chr6:33546651-33546661 chr6:33546651-33546660 chr6:33546651-33546665 chr6:33546650-33546662 chr6:33546606-33546620 chr6:33546650-33546662 chr6:33546651-33546661
26	CTCF	chr6:33546519-33546714	GM12892	blood:	n/a	chr6:33546607-33546620
27	CTCF	chr6:33546700-33546850	GM12865	blood:	n/a	n/a
28	MAX	chr6:33546314-33546855	GM12878	blood:	n/a	chr6:33546610-33546620
29	TCF3	chr6:33546606-33546961	GM12878	blood:	n/a	n/a
30	CTCF	chr6:33546580-33546730	GM12875	blood:	n/a	chr6:33546607-33546620
31	RCOR1	chr6:33545981-33546835	GM12878	blood:	n/a	n/a
32	ELF1	chr6:33546298-33546747	GM12878	blood:	n/a	n/a
33	ELF1	chr6:33546267-33546996	GM12878	blood:	n/a	n/a
34	ATF2	chr6:33546555-33546874	GM12878	blood:	n/a	n/a
35	CTCF	chr6:33546440-33546732	GM12878	blood:	n/a	chr6:33546607-33546620 chr6:33546474-33546482
36	POLR2A	chr6:33546274-33546882	GM12878	blood:	n/a	n/a
37	STAT5A	chr6:33546017-33546836	GM12878	blood:	n/a	chr6:33546647-33546659 chr6:33546520-33546531 chr6:33546612-33546624
38	RUNX3	chr6:33545891-33546782	GM12878	blood:	n/a	n/a
39	IRF1	chr6:33546031-33546725	K562	blood:	n/a	chr6:33546523-33546537 chr6:33546520-33546533 chr6:33546648-33546662 chr6:33546520-33546531 chr6:33546525-33546536 chr6:33546515-33546536 chr6:33546520-33546533 chr6:33546526-33546538 chr6:33546520-33546534 chr6:33546519-33546533 chr6:33546520-33546533 chr6:33546521-33546531 chr6:33546526-33546537 chr6:33546519-33546539 chr6:33546521-33546535
40	POLR2A	chr6:33546211-33546872	GM19193	blood:	n/a	n/a
41	IRF1	chr6:33546315-33546714	K562	blood:	n/a	chr6:33546523-33546537 chr6:33546520-33546533 chr6:33546648-33546662 chr6:33546520-33546531 chr6:33546525-33546536 chr6:33546515-33546536 chr6:33546520-33546533 chr6:33546526-33546538 chr6:33546520-33546534 chr6:33546519-33546533 chr6:33546520-33546533 chr6:33546521-33546531 chr6:33546526-33546537 chr6:33546519-33546539 chr6:33546521-33546535
42	YY1	chr6:33546424-33546738	GM12878	blood:	n/a	chr6:33546461-33546472
43	EBF1	chr6:33546388-33546857	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33381203..33384118-chr6:33546265..33549089,2	K562	blood:
2	chr6:33391848..33395045-chr6:33544542..33547433,3	MCF-7	breast:
3	chr6:33545816..33547496-chr6:33675270..33677360,2	K562	blood:
4	chr6:33420831..33423204-chr6:33545367..33547352,2	MCF-7	breast:
5	chr6:33546298..33549471-chr6:33550091..33553469,5	K562	blood:
6	chr6:33541749..33544429-chr6:33546198..33547784,2	MCF-7	breast:
7	chr6:33420326..33423381-chr6:33545501..33547721,3	MCF-7	breast:
8	chr6:33546546..33549178-chr6:33588334..33590241,2	K562	blood:

Variant related genes	Relation type
GGNBP1	TF binding region
ENSG00000213588	Chromatin interaction
ENSG00000096433	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000204188	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11964131	1.00[AMR][1000 genomes]
rs3846856	1.00[AMR][1000 genomes]
rs3846857	1.00[AMR][1000 genomes]
rs3846858	1.00[AMR][1000 genomes]
rs3846859	1.00[AMR][1000 genomes]
rs3857560	1.00[AMR][1000 genomes]
rs4460206	1.00[AMR][1000 genomes]
rs5745578	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5745579	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5745597	1.00[AMR][1000 genomes]
rs60691479	1.00[AMR][1000 genomes]
rs6903143	1.00[AMR][1000 genomes]
rs6909769	1.00[AMR][1000 genomes]
rs6928531	1.00[AMR][1000 genomes]
rs7744691	1.00[AMR][1000 genomes]
rs7761085	1.00[AMR][1000 genomes]
rs7762586	1.00[AMR][1000 genomes]
rs7765464	1.00[AMR][1000 genomes]
rs7769914	0.84[AFR][1000 genomes];1.00[AMR][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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr6:33539200-33547200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33539600-33547000	Weak transcription	Fetal Kidney	kidney
3	chr6:33539800-33547000	Weak transcription	Psoas Muscle	Psoas
4	chr6:33543400-33547000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:33543400-33547200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:33543600-33547200	Weak transcription	HSMMtube	muscle
7	chr6:33544000-33547200	Weak transcription	Ovary	ovary
8	chr6:33544400-33547000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:33544600-33546800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:33544600-33547400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:33544600-33547600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr6:33544800-33546800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:33544800-33548000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:33545200-33546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr6:33545200-33546800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
16	chr6:33545200-33546800	Enhancers	HUVEC	blood vessel
17	chr6:33545200-33547000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:33545200-33547200	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:33545400-33546800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:33545400-33547200	Weak transcription	Aorta	Aorta
21	chr6:33545400-33547200	Enhancers	Pancreas	Pancrea
22	chr6:33545400-33547800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:33545600-33546800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:33545600-33547000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:33545600-33547600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr6:33545600-33548200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr6:33545800-33546800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:33545800-33547000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:33545800-33547000	Flanking Active TSS	Esophagus	oesophagus
30	chr6:33545800-33547600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:33545800-33547800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:33546000-33546800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:33546000-33546800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:33546000-33546800	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr6:33546000-33546800	Enhancers	Colon Smooth Muscle	Colon
36	chr6:33546000-33546800	Flanking Active TSS	Stomach Mucosa	stomach
37	chr6:33546000-33547000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:33546000-33547000	Enhancers	Brain Germinal Matrix	brain
39	chr6:33546000-33547000	Enhancers	Fetal Brain Female	brain
40	chr6:33546000-33547200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:33546000-33547200	Enhancers	Fetal Heart	heart
42	chr6:33546000-33547400	Flanking Active TSS	Fetal Thymus	thymus
43	chr6:33546000-33547600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr6:33546000-33548000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr6:33546000-33548200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:33546000-33548200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr6:33546000-33548200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:33546000-33548400	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr6:33546200-33546800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr6:33546200-33546800	Transcr. at gene 5' and 3'	NHLF	lung

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