Variant report

Variant	rs4646788
Chromosome Location	chr17:19649073-19649074
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	CEBPB	chr17:19648646-19649256	Hela-S3	cervix:	n/a	n/a
3	RAD21	chr17:19648845-19649302	Hela-S3	cervix:	n/a	n/a
4	REST	chr17:19648225-19649428	A549	lung:	n/a	chr17:19648844-19648864
5	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
6	EP300	chr17:19648146-19649406	A549	lung:	n/a	n/a
7	ATF3	chr17:19648205-19649320	A549	lung:	n/a	n/a
8	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
9	POLR2A	chr17:19648198-19649104	A549	lung:	n/a	n/a
10	SIN3AK20	chr17:19648221-19649189	A549	lung:	n/a	n/a
11	MAX	chr17:19648079-19649538	A549	lung:	n/a	chr17:19648221-19648230 chr17:19648968-19648984
12	STAT3	chr17:19648863-19649080	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr17:19647727-19649157	A549	lung:	n/a	n/a
14	ELF1	chr17:19648764-19649427	A549	lung:	n/a	n/a
15	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
16	BCL3	chr17:19648208-19649440	A549	lung:	n/a	n/a
17	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
18	E2F6	chr17:19648240-19649172	A549	lung:	n/a	chr17:19648597-19648609
19	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
20	JUND	chr17:19648221-19649114	A549	lung:	n/a	chr17:19648607-19648618
21	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
22	MAX	chr17:19648688-19649364	Hela-S3	cervix:	n/a	chr17:19648968-19648984
23	YY1	chr17:19648185-19649206	A549	lung:	n/a	chr17:19648207-19648218
24	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
25	MYC	chr17:19648872-19649093	MCF10A-Er-Src	breast:	n/a	chr17:19648968-19648984
26	REST	chr17:19648132-19649529	A549	lung:	n/a	chr17:19648844-19648864
27	FOXA2	chr17:19648974-19649517	A549	lung:	n/a	n/a
28	POLR2A	chr17:19647668-19649199	A549	lung:	n/a	n/a
29	POLR2A	chr17:19648221-19649087	A549	lung:	n/a	n/a
30	MYC	chr17:19648804-19649135	MCF10A-Er-Src	breast:	n/a	chr17:19648968-19648984
31	STAT3	chr17:19648811-19649181	MCF10A-Er-Src	breast:	n/a	n/a
32	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
33	E2F6	chr17:19648220-19649328	A549	lung:	n/a	chr17:19648597-19648609
34	SIX5	chr17:19648179-19649294	A549	lung:	n/a	n/a
35	E2F6	chr17:19647733-19649136	H1-hESC	embryonic stem cell:	n/a	chr17:19648597-19648609
36	ETS1	chr17:19648210-19649386	A549	lung:	n/a	chr17:19648561-19648577
37	PBX3	chr17:19647746-19649195	A549	lung:	n/a	n/a
38	MYC	chr17:19647731-19649643	A549	lung:	n/a	chr17:19648221-19648230 chr17:19648968-19648984

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:19649051-19649101	NH-A	brain:	n/a
2	chr17:19649051-19649101	SK-N-MC	brain:	n/a
3	chr17:19649051-19649101	HCPEpiC	choroid plexus:	n/a
4	chr17:19649051-19649101	U87	brain:	n/a
5	chr17:19649051-19649101	HEK293	kidney:	embryo
6	chr17:19649051-19649101	IMR90	lung:	fetal
7	chr17:19649051-19649101	AG10803	skin:	n/a
8	chr17:19649051-19649101	A549	lung:	n/a
9	chr17:19649051-19649101	Hepatocyte	liver:	n/a
10	chr17:19649051-19649101	AoSMC	blood vessel:	n/a
11	chr17:19649051-19649101	T-47D	breast:	n/a
12	chr17:19649051-19649101	NHDF-neo	bronchial:	n/a
13	chr17:19649051-19649101	GM06990	blood:	n/a
14	chr17:19649051-19649101	SK-N-SH_RA	brain:	n/a
15	chr17:19649051-19649101	SKMC	muscle:	n/a
16	chr17:19649051-19649101	PFSK-1	brain:	n/a
17	chr17:19649051-19649101	HL-60	blood:	n/a
18	chr17:19649051-19649101	AG04449	skin:	fetal
19	chr17:19649051-19649101	AG09319	gingival:	n/a
20	chr17:19649051-19649101	BJ	skin:	n/a
21	chr17:19649051-19649101	ProgFib	skin:	n/a
22	chr17:19649051-19649101	CMK	blood:	n/a
23	chr17:19649051-19649101	NB4	blood:	n/a
24	chr17:19649051-19649101	GM12878	blood:	n/a
25	chr17:19649051-19649101	SK-N-SH	brain:	n/a
26	chr17:19649051-19649101	RPTEC	kidney:	n/a
27	chr17:19649051-19649101	NHBE	bronchial:	n/a
28	chr17:19649051-19649101	HEEpiC	esophagus:	n/a
29	chr17:19649051-19649101	AG04450	lung:	fetal
30	chr17:19649051-19649101	Hela-S3	cervix:	n/a
31	chr17:19649051-19649101	HCT-116	colon:	n/a
32	chr17:19649051-19649101	Jurkat	blood:	n/a
33	chr17:19649051-19649101	ECC-1	luminal epithelium:	n/a
34	chr17:19649051-19649101	MCF10A-Er-Src	breast:	n/a
35	chr17:19649051-19649101	MCF-7	breast:	n/a
36	chr17:19649051-19649101	HMEC	breast:	n/a
37	chr17:19649051-19649101	PANC-1	pancreas:	n/a
38	chr17:19649051-19649101	HNPCEpiC	eye:	n/a
39	chr17:19649051-19649101	HRE	kidney:	n/a
40	chr17:19649051-19649101	SAEC	small airway:	n/a
41	chr17:19649051-19649101	HPAEpiC	pulmonary alveolar:	n/a
42	chr17:19649051-19649101	GM12891	blood:	n/a
43	chr17:19649051-19649101	GM12892	blood:	n/a
44	chr17:19649051-19649101	BE2_C	brain:	n/a
45	chr17:19649051-19649101	LNCaP	prostate:	n/a
46	chr17:19649051-19649101	HRCEpiC	kidney:	n/a
47	chr17:19649051-19649101	NT2-D1	testis:	n/a
48	chr17:19649051-19649101	PrEC	prostate:	n/a
49	chr17:19649051-19649101	HAEpiC	amniotic membrane:	n/a
50	chr17:19649051-19649101	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19647645..19649705-chr17:19651744..19653267,2	MCF-7	breast:
2	chr11:67372621..67374795-chr17:19647401..19649907,2	MCF-7	breast:
3	chr17:19645239..19646933-chr17:19648650..19650817,2	MCF-7	breast:

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

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1986269	0.90[AMR][1000 genomes]
rs2072328	1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs3744695	0.80[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4646786	1.00[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs4646790	0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs57619378	0.90[AMR][1000 genomes]
rs59204628	1.00[AMR][1000 genomes]
rs59910766	0.90[AMR][1000 genomes]
rs61738931	1.00[AMR][1000 genomes]
rs887240	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs917520	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9895491	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:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19645600-19650800	Weak transcription	Gastric	stomach
2	chr17:19647800-19649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:19647800-19649200	Enhancers	Fetal Heart	heart
4	chr17:19647800-19649400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:19647800-19649800	Enhancers	GM12878-XiMat	blood
6	chr17:19648200-19649400	Enhancers	HMEC	breast
7	chr17:19648400-19649200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:19648400-19649200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr17:19648400-19649200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:19648400-19649200	Flanking Active TSS	NHEK	skin
11	chr17:19648400-19649400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr17:19648400-19649400	Flanking Active TSS	Stomach Mucosa	stomach
13	chr17:19648600-19649200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr17:19648600-19649200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:19648600-19649200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr17:19648600-19649200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:19648600-19649200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:19648600-19649200	Enhancers	Brain Substantia Nigra	brain
19	chr17:19648600-19649400	Transcr. at gene 5' and 3'	A549	lung
20	chr17:19648600-19649600	Flanking Active TSS	Hela-S3	cervix
21	chr17:19648600-19651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:19648600-19651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:19648600-19651800	Weak transcription	HSMM	muscle
24	chr17:19648800-19649200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr17:19648800-19649200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr17:19648800-19649200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr17:19648800-19649200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:19648800-19649200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:19648800-19649200	Enhancers	Adipose Nuclei	Adipose
30	chr17:19648800-19649200	Enhancers	Fetal Lung	lung
31	chr17:19648800-19649200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr17:19648800-19649400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:19648800-19649400	Enhancers	Fetal Intestine Large	intestine
34	chr17:19648800-19649400	Enhancers	Fetal Intestine Small	intestine
35	chr17:19648800-19650000	Weak transcription	Liver	Liver
36	chr17:19648800-19650000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr17:19648800-19650600	Enhancers	Esophagus	oesophagus
38	chr17:19648800-19651200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr17:19648800-19651200	Enhancers	HepG2	liver
40	chr17:19648800-19651400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr17:19648800-19652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
43	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
45	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
46	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
47	chr17:19649000-19649200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
48	chr17:19649000-19649200	Enhancers	Brain Hippocampus Middle	brain
49	chr17:19649000-19649200	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr17:19649000-19649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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