Variant report

Variant	rs4646789
Chromosome Location	chr17:19648629-19648630
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	CTCF	chr17:19648560-19648710	GM12866	blood:	n/a	n/a
2	BCL3	chr17:19647775-19653407	A549	lung:	n/a	chr17:19652977-19652986 chr17:19650882-19650891 chr17:19650661-19650670 chr17:19652047-19652060
3	CTCF	chr17:19648580-19648730	GM12875	blood:	n/a	n/a
4	RAD21	chr17:19648242-19648634	A549	lung:	n/a	chr17:19648461-19648475
5	JUND	chr17:19648224-19648711	H1-hESC	embryonic stem cell:	n/a	chr17:19648607-19648618
6	E2F6	chr17:19647844-19648949	H1-hESC	embryonic stem cell:	n/a	chr17:19648597-19648609
7	REST	chr17:19648225-19649428	A549	lung:	n/a	chr17:19648844-19648864
8	ZBTB33	chr17:19648358-19649032	A549	lung:	n/a	n/a
9	CTCF	chr17:19648615-19648666	Kidney_OC	kidney:	n/a	n/a
10	ELF1	chr17:19648179-19648635	A549	lung:	n/a	n/a
11	CREB1	chr17:19648128-19648982	A549	lung:	n/a	n/a
12	PBX3	chr17:19648208-19648748	A549	lung:	n/a	n/a
13	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
14	EP300	chr17:19648146-19649406	A549	lung:	n/a	n/a
15	ATF3	chr17:19648205-19649320	A549	lung:	n/a	n/a
16	TAF7	chr17:19648090-19648785	H1-hESC	embryonic stem cell:	n/a	n/a
17	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
18	YY1	chr17:19648071-19648793	H1-hESC	embryonic stem cell:	n/a	chr17:19648207-19648218
19	POLR2A	chr17:19648198-19649104	A549	lung:	n/a	n/a
20	CTCF	chr17:19648600-19648750	GM12866	blood:	n/a	n/a
21	SIN3AK20	chr17:19648221-19649189	A549	lung:	n/a	n/a
22	MAX	chr17:19648079-19649538	A549	lung:	n/a	chr17:19648221-19648230 chr17:19648968-19648984
23	CTCF	chr17:19648041-19648676	HCT-116	colon:	n/a	n/a
24	POLR2A	chr17:19647727-19649157	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	FOXA2	chr17:19648187-19648653	A549	lung:	n/a	n/a
27	MAX	chr17:19648260-19648854	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr17:19647836-19648677	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr17:19648195-19648630	H1-hESC	embryonic stem cell:	n/a	chr17:19648207-19648218
30	POLR2A	chr17:19648224-19649058	A549	lung:	n/a	n/a
31	ELF1	chr17:19647745-19648641	GM12878	blood:	n/a	n/a
32	GTF2F1	chr17:19648210-19648740	H1-hESC	embryonic stem cell:	n/a	n/a
33	SIN3A	chr17:19647944-19648908	H1-hESC	embryonic stem cell:	n/a	chr17:19648691-19648702
34	BCL3	chr17:19648208-19649440	A549	lung:	n/a	n/a
35	MYC	chr17:19648244-19648704	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
37	E2F6	chr17:19648240-19649172	A549	lung:	n/a	chr17:19648597-19648609
38	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
39	JUND	chr17:19648221-19649114	A549	lung:	n/a	chr17:19648607-19648618
40	MAX	chr17:19648257-19649054	A549	lung:	n/a	chr17:19648968-19648984
41	ZNF143	chr17:19647978-19648630	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
43	RAD21	chr17:19648071-19648697	A549	lung:	n/a	chr17:19648461-19648475
44	YY1	chr17:19648185-19649206	A549	lung:	n/a	chr17:19648207-19648218
45	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
46	MAX	chr17:19647880-19648947	H1-hESC	embryonic stem cell:	n/a	chr17:19648221-19648230
47	REST	chr17:19648132-19649529	A549	lung:	n/a	chr17:19648844-19648864
48	RAD21	chr17:19647721-19648799	SK-N-SH	brain:	n/a	chr17:19648461-19648475
49	POLR2A	chr17:19647668-19649199	A549	lung:	n/a	n/a
50	TCF12	chr17:19648238-19648757	A549	lung:	n/a	chr17:19648468-19648475

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

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

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2072328	0.84[JPT][hapmap];0.92[AMR][1000 genomes]
rs4646786	0.82[JPT][hapmap];0.92[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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19645600-19650800	Weak transcription	Gastric	stomach
2	chr17:19647800-19648800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:19647800-19648800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr17:19647800-19648800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr17:19647800-19648800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:19647800-19648800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:19647800-19648800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:19647800-19648800	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr17:19647800-19648800	Flanking Active TSS	Fetal Muscle Leg	muscle
10	chr17:19647800-19648800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr17:19647800-19649000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr17:19647800-19649000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:19647800-19649000	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr17:19647800-19649000	Enhancers	Fetal Brain Male	brain
15	chr17:19647800-19649000	Active TSS	Rectal Smooth Muscle	rectum
16	chr17:19647800-19649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:19647800-19649200	Enhancers	Fetal Heart	heart
18	chr17:19647800-19649400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:19647800-19649800	Enhancers	GM12878-XiMat	blood
20	chr17:19648000-19648800	Enhancers	Liver	Liver
21	chr17:19648000-19648800	Enhancers	Spleen	Spleen
22	chr17:19648000-19649000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr17:19648000-19649000	Enhancers	Placenta	Placenta
24	chr17:19648200-19648800	Enhancers	Primary B cells from cord blood	blood
25	chr17:19648200-19649400	Enhancers	HMEC	breast
26	chr17:19648400-19648800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr17:19648400-19648800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
28	chr17:19648400-19648800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:19648400-19648800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:19648400-19648800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr17:19648400-19648800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:19648400-19648800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr17:19648400-19648800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr17:19648400-19648800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr17:19648400-19648800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr17:19648400-19648800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr17:19648400-19648800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr17:19648400-19648800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:19648400-19648800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr17:19648400-19648800	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr17:19648400-19648800	Flanking Active TSS	Colonic Mucosa	Colon
42	chr17:19648400-19648800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr17:19648400-19648800	Flanking Active TSS	Esophagus	oesophagus
44	chr17:19648400-19648800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr17:19648400-19648800	Flanking Active TSS	Fetal Brain Female	brain
46	chr17:19648400-19648800	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr17:19648400-19648800	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr17:19648400-19648800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
49	chr17:19648400-19648800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
50	chr17:19648400-19648800	Flanking Active TSS	Ovary	ovary

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