Variant report

Variant	rs4646783
Chromosome Location	chr17:19652366-19652367
allele	A/C/G/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	NFIC	chr17:19651425-19652701	ECC-1	luminal epithelium:	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	JUND	chr17:19649752-19652440	A549	lung:	n/a	chr17:19652091-19652103 chr17:19652089-19652100
4	MAX	chr17:19651723-19652616	ECC-1	luminal epithelium:	n/a	chr17:19651879-19651888
5	CEBPB	chr17:19651285-19652664	A549	lung:	n/a	n/a
6	POLR2A	chr17:19651813-19652503	A549	lung:	n/a	n/a
7	FOXA2	chr17:19650836-19652908	A549	lung:	n/a	n/a
8	TAF1	chr17:19650416-19652480	A549	lung:	n/a	n/a
9	REST	chr17:19649555-19652980	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
10	TCF12	chr17:19647575-19653308	A549	lung:	n/a	chr17:19648161-19648171 chr17:19648468-19648475 chr17:19648978-19648985 chr17:19651904-19651912
11	MAX	chr17:19652162-19652639	ECC-1	luminal epithelium:	n/a	n/a
12	SIX5	chr17:19650107-19653086	A549	lung:	n/a	n/a
13	SIN3AK20	chr17:19650460-19652543	A549	lung:	n/a	n/a
14	POLR2A	chr17:19649543-19652557	A549	lung:	n/a	n/a
15	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
16	ZBTB7A	chr17:19651350-19652402	ECC-1	luminal epithelium:	n/a	n/a
17	TCF12	chr17:19651355-19652894	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
18	FOXA2	chr17:19650548-19652534	A549	lung:	n/a	n/a
19	E2F6	chr17:19650119-19653193	A549	lung:	n/a	chr17:19652359-19652371
20	MAX	chr17:19652361-19652550	Hela-S3	cervix:	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	EP300	chr17:19651449-19652603	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19651785-19651795
24	POLR2A	chr17:19651836-19652514	A549	lung:	n/a	n/a
25	NFIC	chr17:19651516-19652664	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
27	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
28	TCF12	chr17:19651421-19652649	ECC-1	luminal epithelium:	n/a	chr17:19651904-19651912
29	EP300	chr17:19651454-19652862	ECC-1	luminal epithelium:	n/a	chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
30	SIN3AK20	chr17:19652121-19652634	A549	lung:	n/a	n/a
31	TEAD4	chr17:19651348-19652378	A549	lung:	n/a	n/a
32	EP300	chr17:19649666-19653003	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
33	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
34	FOXM1	chr17:19651455-19652690	ECC-1	luminal epithelium:	n/a	n/a
35	YY1	chr17:19650487-19652390	A549	lung:	n/a	chr17:19652045-19652056 chr17:19651437-19651456
36	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
37	PBX3	chr17:19650460-19652554	A549	lung:	n/a	n/a
38	REST	chr17:19650441-19652474	A549	lung:	n/a	chr17:19650573-19650591 chr17:19652049-19652062 chr17:19652019-19652029
39	EP300	chr17:19649474-19652949	A549	lung:	n/a	chr17:19650306-19650322 chr17:19651055-19651065 chr17:19651868-19651878 chr17:19652732-19652741 chr17:19651785-19651795
40	POLR2A	chr17:19650461-19652561	A549	lung:	n/a	n/a
41	MAX	chr17:19650448-19653274	A549	lung:	n/a	chr17:19651879-19651888
42	E2F6	chr17:19652173-19652569	H1-hESC	embryonic stem cell:	n/a	chr17:19652359-19652371
43	E2F6	chr17:19651750-19652647	A549	lung:	n/a	chr17:19652359-19652371

No.	Distal block	Cell Line	Cell type
1	chr11:67370569..67373136-chr17:19651754..19653561,2	MCF-7	breast:
2	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:
3	chr17:19647645..19649705-chr17:19651744..19653267,2	MCF-7	breast:

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

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11871642	1.00[JPT][hapmap]
rs1585751	1.00[EUR][1000 genomes]
rs16960503	1.00[EUR][1000 genomes]
rs2289666	1.00[JPT][hapmap]
rs28632080	1.00[EUR][1000 genomes]
rs28661916	1.00[EUR][1000 genomes]
rs3744692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3760488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786035	0.94[ASN][1000 genomes]
rs3786037	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56407718	1.00[EUR][1000 genomes]
rs56705977	1.00[EUR][1000 genomes]
rs7216958	1.00[EUR][1000 genomes]
rs8066134	1.00[EUR][1000 genomes]
rs8068565	1.00[EUR][1000 genomes]
rs9890667	1.00[EUR][1000 genomes]
rs9893138	1.00[EUR][1000 genomes]
rs9894723	1.00[EUR][1000 genomes]
rs9899365	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	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
9	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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
2	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
4	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
5	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
6	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
8	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
9	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr17:19649800-19652800	Weak transcription	GM12878-XiMat	blood
11	chr17:19650200-19656800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr17:19650600-19657000	Enhancers	HMEC	breast
13	chr17:19650600-19657600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:19650800-19652400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:19651000-19652400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr17:19651000-19652400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr17:19651000-19652600	Enhancers	Liver	Liver
18	chr17:19651000-19652600	Flanking Active TSS	Hela-S3	cervix
19	chr17:19651000-19656200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:19651200-19652400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr17:19651200-19652400	Enhancers	Brain Cingulate Gyrus	brain
22	chr17:19651200-19652600	Enhancers	Brain Hippocampus Middle	brain
23	chr17:19651200-19652600	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr17:19651200-19653400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:19651200-19654400	Enhancers	NHEK	skin
26	chr17:19651400-19652400	Enhancers	Brain Anterior Caudate	brain
27	chr17:19651400-19652600	Enhancers	Stomach Smooth Muscle	stomach
28	chr17:19651600-19652400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:19651600-19652400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:19651600-19652400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:19651600-19652400	Enhancers	Adipose Nuclei	Adipose
32	chr17:19651600-19652400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr17:19651600-19652400	Enhancers	Pancreas	Pancrea
34	chr17:19651600-19652400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr17:19651600-19652600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr17:19651600-19652600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr17:19651600-19652600	Enhancers	NHDF-Ad	bronchial
38	chr17:19651600-19652800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr17:19651600-19653000	Enhancers	Gastric	stomach
40	chr17:19651600-19654800	Enhancers	Esophagus	oesophagus
41	chr17:19651800-19652400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
42	chr17:19651800-19652400	Enhancers	Brain Germinal Matrix	brain
43	chr17:19651800-19652400	Bivalent Enhancer	Fetal Stomach	stomach
44	chr17:19651800-19652400	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr17:19651800-19653400	Enhancers	Stomach Mucosa	stomach
46	chr17:19652000-19652400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr17:19652000-19652400	Enhancers	Brain Substantia Nigra	brain
48	chr17:19652000-19652600	Flanking Active TSS	A549	lung
49	chr17:19652000-19653400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:19652000-19655400	Weak transcription	HSMMtube	muscle

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