Variant report

Variant	rs4646787
Chromosome Location	chr17:19649249-19649250
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	POLR2A	chr17:19649220-19649507	A549	lung:	n/a	n/a
8	ATF3	chr17:19648205-19649320	A549	lung:	n/a	n/a
9	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
10	MAX	chr17:19648079-19649538	A549	lung:	n/a	chr17:19648221-19648230 chr17:19648968-19648984
11	ELF1	chr17:19648764-19649427	A549	lung:	n/a	n/a
12	CTCF	chr17:19647746-19653300	A549	lung:	n/a	chr17:19648889-19648902 chr17:19650591-19650599 chr17:19651387-19651397 chr17:19649367-19649376
13	POLR2A	chr17:19649237-19649501	A549	lung:	n/a	n/a
14	BCL3	chr17:19648208-19649440	A549	lung:	n/a	n/a
15	MAX	chr17:19648056-19653846	A549	lung:	n/a	chr17:19651879-19651888 chr17:19648221-19648230 chr17:19648968-19648984
16	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
17	FOSL2	chr17:19648208-19652390	A549	lung:	n/a	chr17:19652091-19652103 chr17:19648607-19648618 chr17:19652089-19652100
18	MAX	chr17:19648688-19649364	Hela-S3	cervix:	n/a	chr17:19648968-19648984
19	POLR2A	chr17:19647758-19651715	A549	lung:	n/a	n/a
20	REST	chr17:19648132-19649529	A549	lung:	n/a	chr17:19648844-19648864
21	FOXA2	chr17:19648974-19649517	A549	lung:	n/a	n/a
22	GATA3	chr17:19648106-19652992	A549	lung:	n/a	chr17:19650936-19650945 chr17:19649206-19649217
23	E2F6	chr17:19648220-19649328	A549	lung:	n/a	chr17:19648597-19648609
24	SIX5	chr17:19648179-19649294	A549	lung:	n/a	n/a
25	ETS1	chr17:19648210-19649386	A549	lung:	n/a	chr17:19648561-19648577
26	MYC	chr17:19647731-19649643	A549	lung:	n/a	chr17:19648221-19648230 chr17:19648968-19648984
27	POLR2A	chr17:19649218-19649512	A549	lung:	n/a	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:
4	chr17:19649191..19653636-chr17:19654131..19659903,8	MCF-7	breast:

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

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006554	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11204411	0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11204412	0.90[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11204413	0.87[EUR][1000 genomes]
rs11204414	0.94[EUR][1000 genomes]
rs12942065	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12945122	0.90[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12948735	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs157404	1.00[JPT][hapmap]
rs2108967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs281357	1.00[JPT][hapmap]
rs3744693	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4646784	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs4924793	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4925044	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7209418	0.84[EUR][1000 genomes]
rs7214841	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7221211	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222877	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs8064572	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8077368	0.80[EUR][1000 genomes]
rs887241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9910370	0.81[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19645600-19650800	Weak transcription	Gastric	stomach
2	chr17:19647800-19649400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19647800-19649800	Enhancers	GM12878-XiMat	blood
4	chr17:19648200-19649400	Enhancers	HMEC	breast
5	chr17:19648400-19649400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr17:19648400-19649400	Flanking Active TSS	Stomach Mucosa	stomach
7	chr17:19648600-19649400	Transcr. at gene 5' and 3'	A549	lung
8	chr17:19648600-19649600	Flanking Active TSS	Hela-S3	cervix
9	chr17:19648600-19651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr17:19648600-19651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr17:19648600-19651800	Weak transcription	HSMM	muscle
12	chr17:19648800-19649400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:19648800-19649400	Enhancers	Fetal Intestine Large	intestine
14	chr17:19648800-19649400	Enhancers	Fetal Intestine Small	intestine
15	chr17:19648800-19650000	Weak transcription	Liver	Liver
16	chr17:19648800-19650000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:19648800-19650600	Enhancers	Esophagus	oesophagus
18	chr17:19648800-19651200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr17:19648800-19651200	Enhancers	HepG2	liver
20	chr17:19648800-19651400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr17:19648800-19652200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:19648800-19652600	Enhancers	Duodenum Mucosa	Duodenum
23	chr17:19648800-19654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr17:19648800-19654200	Weak transcription	HUVEC	blood vessel
25	chr17:19648800-19656200	Weak transcription	Aorta	Aorta
26	chr17:19648800-19657000	Weak transcription	Spleen	Spleen
27	chr17:19649000-19649400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:19649000-19649400	Enhancers	Brain Angular Gyrus	brain
29	chr17:19649000-19649400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr17:19649000-19649600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:19649000-19651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr17:19649000-19651200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:19649000-19651400	Weak transcription	Brain Anterior Caudate	brain
34	chr17:19649000-19651600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:19649000-19651600	Weak transcription	Pancreas	Pancrea
36	chr17:19649000-19652600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr17:19649000-19656400	Weak transcription	Right Atrium	heart
38	chr17:19649200-19649400	Enhancers	NHEK	skin
39	chr17:19649200-19649800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:19649200-19651200	Weak transcription	Brain Hippocampus Middle	brain
41	chr17:19649200-19651200	Weak transcription	Brain Substantia Nigra	brain
42	chr17:19649200-19651400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:19649200-19651400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:19649200-19651400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr17:19649200-19651600	Weak transcription	Adipose Nuclei	Adipose
46	chr17:19649200-19651600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr17:19649200-19652600	Enhancers	Colonic Mucosa	Colon
48	chr17:19649200-19656200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links