Variant report

Variant	rs58060020
Chromosome Location	chr17:19651383-19651384
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	BCL3	chr17:19647775-19653407	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650882-19650891 chr17:19650661-19650670 chr17:19652047-19652060
2	JUND	chr17:19649752-19652440	A549	lung:	n/a	chr17:19652091-19652103 chr17:19652089-19652100
3	CEBPB	chr17:19651285-19652664	A549	lung:	n/a	n/a
4	ZBTB33	chr17:19650426-19652363	A549	lung:	n/a	n/a
5	TCF12	chr17:19650454-19652262	A549	lung:	n/a	chr17:19651904-19651912
6	FOXA2	chr17:19650836-19652908	A549	lung:	n/a	n/a
7	TAF1	chr17:19650416-19652480	A549	lung:	n/a	n/a
8	REST	chr17:19649555-19652980	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
9	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
10	POLR2A	chr17:19650477-19651757	A549	lung:	n/a	n/a
11	SIX5	chr17:19650107-19653086	A549	lung:	n/a	n/a
12	SIN3AK20	chr17:19650460-19652543	A549	lung:	n/a	n/a
13	POLR2A	chr17:19649543-19652557	A549	lung:	n/a	n/a
14	SP1	chr17:19648147-19652905	A549	lung:	n/a	chr17:19650262-19650269 chr17:19648213-19648225 chr17:19648215-19648224 chr17:19650286-19650300 chr17:19648214-19648223 chr17:19648209-19648223 chr17:19648214-19648224 chr17:19648492-19648506 chr17:19648223-19648233 chr17:19648213-19648225 chr17:19648214-19648228
15	ZBTB7A	chr17:19651350-19652402	ECC-1	luminal epithelium:	n/a	n/a
16	TCF12	chr17:19651355-19652894	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
17	NR3C1	chr17:19650631-19652321	A549	lung:	n/a	chr17:19650710-19650717
18	FOXA2	chr17:19650548-19652534	A549	lung:	n/a	n/a
19	E2F6	chr17:19650119-19653193	A549	lung:	n/a	chr17:19652359-19652371
20	ETS1	chr17:19650619-19652279	A549	lung:	n/a	n/a
21	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
22	MAX	chr17:19651150-19652545	A549	lung:	n/a	chr17:19651879-19651888
23	POLR2A	chr17:19650474-19651812	A549	lung:	n/a	n/a
24	RFX5	chr17:19651332-19652088	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr17:19651236-19652162	A549	lung:	n/a	chr17:19651386-19651396
26	ATF3	chr17:19650727-19652245	A549	lung:	n/a	n/a
27	ELF1	chr17:19649892-19652087	A549	lung:	n/a	chr17:19650152-19650163
28	ZBTB33	chr17:19650486-19652351	A549	lung:	n/a	n/a
29	RCOR1	chr17:19651367-19651984	Hela-S3	cervix:	n/a	n/a
30	NR3C1	chr17:19651171-19652186	A549	lung:	n/a	n/a
31	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
32	SP1	chr17:19648113-19653000	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650262-19650269 chr17:19648213-19648225 chr17:19648215-19648224 chr17:19650286-19650300 chr17:19652976-19652985 chr17:19648214-19648223 chr17:19648209-19648223 chr17:19652975-19652987 chr17:19648214-19648224 chr17:19648492-19648506 chr17:19648223-19648233 chr17:19648213-19648225 chr17:19648214-19648228
33	USF1	chr17:19649934-19652251	A549	lung:	n/a	n/a
34	PBX3	chr17:19650471-19652146	A549	lung:	n/a	n/a
35	TEAD4	chr17:19651348-19652378	A549	lung:	n/a	n/a
36	EP300	chr17:19649666-19653003	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
37	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
38	CREB1	chr17:19651122-19652286	A549	lung:	n/a	n/a
39	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
40	TEAD4	chr17:19651306-19652166	A549	lung:	n/a	n/a
41	GABPA	chr17:19651085-19652352	A549	lung:	n/a	n/a
42	ATF3	chr17:19650542-19652172	A549	lung:	n/a	n/a
43	NR3C1	chr17:19650870-19652284	A549	lung:	n/a	n/a
44	YY1	chr17:19650487-19652390	A549	lung:	n/a	chr17:19652045-19652056 chr17:19651437-19651456
45	SIN3AK20	chr17:19650828-19652025	A549	lung:	n/a	n/a
46	ETS1	chr17:19650417-19652124	A549	lung:	n/a	n/a
47	FOSL2	chr17:19651349-19652133	A549	lung:	n/a	chr17:19652091-19652103 chr17:19652089-19652100
48	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
49	POLR2A	chr17:19650443-19651808	A549	lung:	n/a	n/a
50	PBX3	chr17:19650460-19652554	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19641924..19645093-chr17:19650303..19652085,4	MCF-7	breast:
2	chr11:67372115..67374476-chr17:19649917..19652325,2	MCF-7	breast:
3	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:

Variant related genes	Relation type
ALDH3A1	TF binding region
ENSG00000167792	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000184224	Chromatin interaction
ENSG00000255119	Chromatin interaction
ENSG00000108602	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16960349	1.00[AMR][1000 genomes]
rs58072200	1.00[AMR][1000 genomes]
rs58851845	1.00[AMR][1000 genomes]
rs60739355	1.00[AMR][1000 genomes]
rs73295810	1.00[AMR][1000 genomes]
rs887238	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv1807724	chr17:19597423-19656009	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv1793043	chr17:19604821-19670329	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv526290	chr17:19613357-19651482	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv457704	chr17:19620477-19663747	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv470582	chr17:19620477-19663747	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv574580	chr17:19620477-19663747	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648600-19651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr17:19648600-19651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr17:19648600-19651800	Weak transcription	HSMM	muscle
4	chr17:19648800-19651400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:19648800-19652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
7	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
9	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
10	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
11	chr17:19649000-19651400	Weak transcription	Brain Anterior Caudate	brain
12	chr17:19649000-19651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:19649000-19651600	Weak transcription	Pancreas	Pancrea
14	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
16	chr17:19649200-19651400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:19649200-19651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:19649200-19651400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:19649200-19651600	Weak transcription	Adipose Nuclei	Adipose
20	chr17:19649200-19651600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
22	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:19649400-19651400	Weak transcription	Brain Angular Gyrus	brain
24	chr17:19649400-19651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:19649800-19652800	Weak transcription	GM12878-XiMat	blood
26	chr17:19650200-19651600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr17:19650600-19651600	Flanking Active TSS	Esophagus	oesophagus
29	chr17:19650600-19657000	Enhancers	HMEC	breast
30	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:19650800-19651400	Flanking Active TSS	Stomach Mucosa	stomach
32	chr17:19650800-19651400	Transcr. at gene 5' and 3'	A549	lung
33	chr17:19650800-19652400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:19651000-19652200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr17:19651000-19652400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr17:19651000-19652400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr17:19651000-19652600	Enhancers	Liver	Liver
38	chr17:19651000-19652600	Flanking Active TSS	Hela-S3	cervix
39	chr17:19651000-19656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:19651200-19651400	Enhancers	Lung	lung
41	chr17:19651200-19651600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr17:19651200-19651600	Enhancers	Brain Substantia Nigra	brain
43	chr17:19651200-19651600	Flanking Active TSS	Gastric	stomach
44	chr17:19651200-19651800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
45	chr17:19651200-19651800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr17:19651200-19652200	Enhancers	Fetal Intestine Small	intestine
47	chr17:19651200-19652200	Flanking Active TSS	HepG2	liver
48	chr17:19651200-19652400	Enhancers	Muscle Satellite Cultured Cells	--
49	chr17:19651200-19652400	Enhancers	Brain Cingulate Gyrus	brain
50	chr17:19651200-19652600	Enhancers	Brain Hippocampus Middle	brain

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