Variant report

Variant	rs35795560
Chromosome Location	chr17:46047938-46047939
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	MAX	chr17:46047601-46049109	NB4	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
2	EP300	chr17:46047914-46048560	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr17:46047925-46048388	HepG2	liver:	n/a	chr17:46048248-46048258
4	POLR2A	chr17:46047860-46049148	PANC-1	pancreas:	n/a	n/a
5	MAX	chr17:46047776-46049210	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
6	MAX	chr17:46047898-46049065	GM12878	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
7	SP1	chr17:46047927-46048696	HepG2	liver:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
8	ZNF143	chr17:46047928-46048797	K562	blood:	n/a	n/a
9	FOSL1	chr17:46047792-46048669	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
10	ELF1	chr17:46047860-46048985	GM12878	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
11	CBX3	chr17:46047908-46049109	K562	blood:	n/a	n/a
12	SP1	chr17:46047685-46049130	A549	lung:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
13	RAD21	chr17:46047907-46048388	H1-hESC	embryonic stem cell:	n/a	chr17:46048248-46048258
14	POLR2A	chr17:46047890-46048934	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr17:46047909-46049047	HCT-116	colon:	n/a	n/a
16	REST	chr17:46047896-46048649	HepG2	liver:	n/a	n/a
17	BCL3	chr17:46047711-46049097	A549	lung:	n/a	chr17:46048226-46048239 chr17:46048495-46048504
18	ZNF263	chr17:46047886-46048920	HEK293-T-REx	kidney:	n/a	n/a
19	TAF1	chr17:46047893-46048764	GM12878	blood:	n/a	n/a
20	MBD4	chr17:46047816-46048986	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:46047904-46049016	H1-neurons	neurons:	n/a	n/a
22	KAP1	chr17:46047778-46048909	HEK293	kidney:	n/a	n/a
23	POLR2A	chr17:46047938-46048748	HCT-116	colon:	n/a	n/a
24	CHD2	chr17:46047834-46048730	GM12878	blood:	n/a	n/a
25	ATF2	chr17:46047880-46048344	H1-hESC	embryonic stem cell:	n/a	n/a
26	PML	chr17:46047903-46049056	MCF-7	breast:	n/a	n/a
27	SP1	chr17:46047640-46049097	HCT-116	colon:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
28	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
29	MAX	chr17:46047592-46049187	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
30	BHLHE40	chr17:46047927-46048950	HepG2	liver:	n/a	chr17:46048792-46048808
31	CTCF	chr17:46047932-46048386	H1-hESC	embryonic stem cell:	n/a	chr17:46048168-46048177
32	NFIC	chr17:46047884-46048657	HepG2	liver:	n/a	chr17:46048154-46048182
33	RCOR1	chr17:46047602-46048930	HepG2	liver:	n/a	n/a
34	TEAD4	chr17:46047779-46048493	HepG2	liver:	n/a	n/a
35	SP1	chr17:46047722-46049009	A549	lung:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
36	ARID3A	chr17:46047736-46048919	HepG2	liver:	n/a	n/a
37	SIN3AK20	chr17:46047905-46048311	H1-hESC	embryonic stem cell:	n/a	n/a
38	POU2F2	chr17:46047906-46048803	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:46047896-46048951	HepG2	liver:	n/a	n/a
40	SP1	chr17:46047890-46048688	GM12878	blood:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
41	USF1	chr17:46047845-46048912	A549	lung:	n/a	chr17:46048792-46048808
42	ELF1	chr17:46047765-46049043	MCF-7	breast:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
43	SP1	chr17:46047935-46048596	K562	blood:	n/a	chr17:46048298-46048312 chr17:46048335-46048347 chr17:46048337-46048346 chr17:46048336-46048346 chr17:46048269-46048290 chr17:46048335-46048347 chr17:46048464-46048473 chr17:46048469-46048478 chr17:46048336-46048345 chr17:46048336-46048346
44	YY1	chr17:46047938-46048725	HCT-116	colon:	n/a	n/a
45	MAZ	chr17:46047831-46048973	K562	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
46	CEBPB	chr17:46047858-46048905	GM12878	blood:	n/a	chr17:46048373-46048381
47	RUNX3	chr17:46047777-46048941	GM12878	blood:	n/a	chr17:46047800-46047815
48	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr17:46047930-46048931	GM18505	blood:	n/a	n/a
50	BCLAF1	chr17:46047924-46049035	GM12878	blood:	n/a	chr17:46048226-46048239 chr17:46048495-46048504

No.	Distal block	Cell Line	Cell type
1	chr17:46046297..46048098-chr17:46050701..46053030,2	MCF-7	breast:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
4	chr11:64510615..64511340-chr17:46047851..46048383,2	MCF-7	breast:
5	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
6	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
7	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
8	chr17:45917404..45919085-chr17:46045221..46048078,2	K562	blood:
9	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
10	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
11	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
12	chr17:45727256..45728937-chr17:46047807..46049675,2	K562	blood:
13	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
14	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
15	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
16	chr17:46034698..46035465-chr17:46047687..46048504,2	MCF-7	breast:
17	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
18	chr17:45973269..45974008-chr17:46047794..46048455,3	K562	blood:
19	chr17:46046859..46048450-chr17:46055513..46058232,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12939977	0.81[AFR][1000 genomes]
rs12941306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12942412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944699	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12945362	1.00[AMR][1000 genomes]
rs12945768	1.00[AMR][1000 genomes]
rs12947761	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12947966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12948207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16952687	1.00[AMR][1000 genomes]
rs34033530	1.00[AMR][1000 genomes]
rs34038169	1.00[AMR][1000 genomes]
rs34153693	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34166016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34358803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34601263	1.00[AFR][1000 genomes]
rs34632031	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34822864	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34958507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35177469	1.00[AMR][1000 genomes]
rs35273388	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35350665	1.00[AMR][1000 genomes]
rs35534834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35551276	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35647888	1.00[AMR][1000 genomes]
rs35677091	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35711165	1.00[AMR][1000 genomes]
rs35751035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35766594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35778085	1.00[AMR][1000 genomes]
rs35848720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35928933	1.00[AMR][1000 genomes]
rs36059789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36090279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56078988	1.00[AMR][1000 genomes]
rs56363348	1.00[AMR][1000 genomes]
rs57864674	1.00[AMR][1000 genomes]
rs57948485	1.00[AMR][1000 genomes]
rs58974249	1.00[AMR][1000 genomes]
rs59483607	1.00[AMR][1000 genomes]
rs59727791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60224300	1.00[AMR][1000 genomes]
rs60525548	1.00[AMR][1000 genomes]
rs6503951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369826	0.88[AFR][1000 genomes]
rs71377331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377334	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71377338	1.00[AMR][1000 genomes]
rs71377341	1.00[AMR][1000 genomes]
rs71377342	1.00[AMR][1000 genomes]
rs73985416	1.00[AMR][1000 genomes]
rs73985417	1.00[AMR][1000 genomes]
rs73985418	1.00[AMR][1000 genomes]
rs73985419	1.00[AMR][1000 genomes]
rs73985421	1.00[AMR][1000 genomes]
rs73985422	1.00[AMR][1000 genomes]
rs73985424	1.00[AMR][1000 genomes]
rs73985479	1.00[AMR][1000 genomes]
rs8075711	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46044800-46048000	Enhancers	Placenta	Placenta
2	chr17:46045400-46048400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
4	chr17:46047200-46048000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:46047200-46048000	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr17:46047200-46048000	Enhancers	Esophagus	oesophagus
7	chr17:46047200-46048000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr17:46047200-46048400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:46047400-46048000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr17:46047400-46048000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr17:46047400-46048000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr17:46047400-46048000	Flanking Active TSS	Fetal Intestine Small	intestine
13	chr17:46047400-46048200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr17:46047400-46048200	Flanking Active TSS	Dnd41	blood
15	chr17:46047400-46048400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46047400-46049200	Active TSS	Fetal Kidney	kidney
17	chr17:46047600-46048000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:46047600-46048000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr17:46047600-46048000	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr17:46047600-46048000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:46047600-46048000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr17:46047600-46048000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr17:46047600-46048000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:46047600-46048000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:46047600-46048000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr17:46047600-46048000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:46047600-46048000	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr17:46047600-46048000	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr17:46047600-46048000	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr17:46047600-46048000	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr17:46047600-46048000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr17:46047600-46048000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:46047600-46048000	Flanking Active TSS	Colonic Mucosa	Colon
34	chr17:46047600-46048000	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr17:46047600-46048200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:46047600-46048200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:46047600-46048200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr17:46047600-46048200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr17:46047600-46048200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr17:46047600-46048200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr17:46047600-46048200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr17:46047600-46048200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr17:46047600-46048200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr17:46047600-46048200	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr17:46047600-46048200	Flanking Active TSS	Liver	Liver
46	chr17:46047600-46048200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr17:46047600-46048200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr17:46047600-46048200	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr17:46047600-46048200	Flanking Active TSS	A549	lung
50	chr17:46047600-46048200	Flanking Active TSS	K562	blood

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