Variant report

Variant	rs577605521
Chromosome Location	chr17:19649968-19649969
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	TCF3	chr17:19649734-19650232	GM12878	blood:	n/a	n/a
2	CTCF	chr17:19649945-19650056	GM12892	blood:	n/a	n/a
3	POLR2A	chr17:19649810-19650160	GM12892	blood:	n/a	n/a
4	BCL3	chr17:19647775-19653407	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650882-19650891 chr17:19650661-19650670 chr17:19652047-19652060
5	JUND	chr17:19649752-19652440	A549	lung:	n/a	chr17:19652091-19652103 chr17:19652089-19652100
6	ETS1	chr17:19649689-19650232	A549	lung:	n/a	n/a
7	MYC	chr17:19649877-19650127	MCF-7	breast:	n/a	n/a
8	PBX3	chr17:19649827-19650134	GM12878	blood:	n/a	n/a
9	BCL3	chr17:19649731-19650246	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:19649824-19650186	A549	lung:	n/a	n/a
11	PAX5	chr17:19649888-19650115	GM12878	blood:	n/a	n/a
12	CREB1	chr17:19649881-19650151	A549	lung:	n/a	n/a
13	POLR2A	chr17:19649899-19650088	MCF-7	breast:	n/a	n/a
14	REST	chr17:19649555-19652980	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
15	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
16	SIN3AK20	chr17:19649529-19650288	A549	lung:	n/a	n/a
17	YY1	chr17:19649831-19650213	A549	lung:	n/a	n/a
18	POU2F2	chr17:19649930-19650078	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:19649543-19652557	A549	lung:	n/a	n/a
20	NFATC1	chr17:19649803-19650287	GM12878	blood:	n/a	n/a
21	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
22	REST	chr17:19649899-19650377	A549	lung:	n/a	n/a
23	POLR2A	chr17:19649834-19650184	A549	lung:	n/a	n/a
24	FOSL2	chr17:19649743-19650198	A549	lung:	n/a	n/a
25	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
26	CEBPB	chr17:19649751-19650446	A549	lung:	n/a	chr17:19650157-19650170
27	POLR2A	chr17:19649642-19650394	A549	lung:	n/a	n/a
28	ELF1	chr17:19649892-19652087	A549	lung:	n/a	chr17:19650152-19650163
29	CTCF	chr17:19649948-19649969	NHEK	skin:	n/a	n/a
30	POLR2A	chr17:19649812-19650162	MCF-7	breast:	n/a	n/a
31	NFATC1	chr17:19649720-19650270	GM12878	blood:	n/a	n/a
32	JUND	chr17:19649759-19650851	A549	lung:	n/a	n/a
33	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
34	CTCF	chr17:19649962-19650027	MCF-7	breast:	n/a	n/a
35	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
36	CTCF	chr17:19649945-19650012	MCF-7	breast:	n/a	n/a
37	USF1	chr17:19649934-19652251	A549	lung:	n/a	n/a
38	EP300	chr17:19649666-19653003	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
39	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
40	CTCF	chr17:19649942-19650009	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr17:19649909-19650072	GM19239	blood:	n/a	n/a
42	STAT5A	chr17:19649816-19650154	GM12878	blood:	n/a	n/a
43	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
44	CEBPB	chr17:19649967-19650290	A549	lung:	n/a	chr17:19650157-19650170
45	POLR2A	chr17:19649840-19650175	A549	lung:	n/a	n/a
46	BCL3	chr17:19649776-19650181	GM12878	blood:	n/a	n/a
47	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
48	TCF3	chr17:19649852-19650100	GM12878	blood:	n/a	n/a
49	MYC	chr17:19649923-19650064	MCF-7	breast:	n/a	n/a
50	EP300	chr17:19649474-19652949	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795

No.	Distal block	Cell Line	Cell type
1	chr11:67372115..67374476-chr17:19649917..19652325,2	MCF-7	breast:
2	chr17:19645239..19646933-chr17:19648650..19650817,2	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
ENSG00000184224	Chromatin interaction
ENSG00000255119	Chromatin interaction
ENSG00000230607	Chromatin interaction
ENSG00000108602	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	esv3439671	chr17:19649881-19650091	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19645600-19650800	Weak transcription	Gastric	stomach
2	chr17:19648600-19651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr17:19648600-19651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:19648600-19651800	Weak transcription	HSMM	muscle
5	chr17:19648800-19650000	Weak transcription	Liver	Liver
6	chr17:19648800-19650000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:19648800-19650600	Enhancers	Esophagus	oesophagus
8	chr17:19648800-19651200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr17:19648800-19651200	Enhancers	HepG2	liver
10	chr17:19648800-19651400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:19648800-19652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
13	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
15	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
16	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
17	chr17:19649000-19651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:19649000-19651200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr17:19649000-19651400	Weak transcription	Brain Anterior Caudate	brain
20	chr17:19649000-19651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:19649000-19651600	Weak transcription	Pancreas	Pancrea
22	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
24	chr17:19649200-19651200	Weak transcription	Brain Hippocampus Middle	brain
25	chr17:19649200-19651200	Weak transcription	Brain Substantia Nigra	brain
26	chr17:19649200-19651400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:19649200-19651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:19649200-19651400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:19649200-19651600	Weak transcription	Adipose Nuclei	Adipose
30	chr17:19649200-19651600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
32	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr17:19649400-19650400	Flanking Active TSS	A549	lung
34	chr17:19649400-19650600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr17:19649400-19650600	Weak transcription	HMEC	breast
36	chr17:19649400-19650800	Enhancers	Stomach Mucosa	stomach
37	chr17:19649400-19651000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr17:19649400-19651200	Weak transcription	Fetal Intestine Small	intestine
39	chr17:19649400-19651200	Weak transcription	NHEK	skin
40	chr17:19649400-19651400	Weak transcription	Brain Angular Gyrus	brain
41	chr17:19649400-19651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:19649600-19650600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:19649600-19651000	Enhancers	Hela-S3	cervix
44	chr17:19649800-19650000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr17:19649800-19650200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr17:19649800-19652800	Weak transcription	GM12878-XiMat	blood

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