Variant report

Variant	rs12947966
Chromosome Location	chr17:46048014-46048015
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	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	chr17:46047943-46049094	K562	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
6	IRF1	chr17:46048010-46048879	K562	blood:	n/a	chr17:46048335-46048349 chr17:46048373-46048382
7	RAD21	chr17:46048007-46048402	Hela-S3	cervix:	n/a	chr17:46048248-46048258
8	ELF1	chr17:46048006-46048933	K562	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
9	MAX	chr17:46047776-46049210	HCT-116	colon:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
10	MAX	chr17:46047898-46049065	GM12878	blood:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
11	JUND	chr17:46047955-46048923	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
12	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
13	ZNF143	chr17:46047928-46048797	K562	blood:	n/a	n/a
14	TAF1	chr17:46047972-46048901	HepG2	liver:	n/a	n/a
15	SMARCB1	chr17:46047953-46049191	Hela-S3	cervix:	n/a	n/a
16	FOSL1	chr17:46047792-46048669	K562	blood:	n/a	chr17:46048467-46048476 chr17:46048371-46048380
17	GTF2F1	chr17:46048004-46048939	K562	blood:	n/a	n/a
18	ELF1	chr17:46047860-46048985	GM12878	blood:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
19	CBX3	chr17:46047908-46049109	K562	blood:	n/a	n/a
20	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
21	PAX5	chr17:46047969-46048388	GM12878	blood:	n/a	n/a
22	RAD21	chr17:46047907-46048388	H1-hESC	embryonic stem cell:	n/a	chr17:46048248-46048258
23	ELF1	chr17:46047954-46049020	SK-N-SH	brain:	n/a	chr17:46048491-46048504 chr17:46048494-46048503
24	JUND	chr17:46047983-46048414	HepG2	liver:	n/a	chr17:46048371-46048380
25	POLR2A	chr17:46047890-46048934	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr17:46047909-46049047	HCT-116	colon:	n/a	n/a
27	REST	chr17:46047896-46048649	HepG2	liver:	n/a	n/a
28	CTCF	chr17:46047980-46048130	HCM	heart:	n/a	n/a
29	TBL1XR1	chr17:46047952-46049041	K562	blood:	n/a	n/a
30	BRCA1	chr17:46048008-46048315	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr17:46047960-46048110	GM12801	blood:	n/a	n/a
32	BCL3	chr17:46047711-46049097	A549	lung:	n/a	chr17:46048226-46048239 chr17:46048495-46048504
33	ELK1	chr17:46047939-46048749	GM12878	blood:	n/a	n/a
34	ZNF263	chr17:46047886-46048920	HEK293-T-REx	kidney:	n/a	n/a
35	TAF1	chr17:46047893-46048764	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:46047957-46048991	GM12878	blood:	n/a	n/a
37	MBD4	chr17:46047816-46048986	HepG2	liver:	n/a	n/a
38	TAF1	chr17:46047940-46048888	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr17:46047904-46049016	H1-neurons	neurons:	n/a	n/a
40	KAP1	chr17:46047778-46048909	HEK293	kidney:	n/a	n/a
41	EGR1	chr17:46047940-46048889	H1-hESC	embryonic stem cell:	n/a	chr17:46048335-46048345 chr17:46048495-46048504 chr17:46048336-46048346 chr17:46048777-46048787
42	POLR2A	chr17:46047938-46048748	HCT-116	colon:	n/a	n/a
43	MAX	chr17:46047941-46049070	A549	lung:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
44	CHD2	chr17:46047834-46048730	GM12878	blood:	n/a	n/a
45	ATF2	chr17:46047880-46048344	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr17:46047955-46048963	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710
47	PML	chr17:46047903-46049056	MCF-7	breast:	n/a	n/a
48	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
49	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
50	MAX	chr17:46047592-46049187	HepG2	liver:	n/a	chr17:46048336-46048346 chr17:46048700-46048710

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
ENSG00000189120	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000068831	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]
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]
rs35795560	1.00[AFR][1000 genomes];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	chr17:46045400-46048400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:46047000-46049400	Active TSS	Rectal Smooth Muscle	rectum
3	chr17:46047200-46048400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:46047400-46048200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr17:46047400-46048200	Flanking Active TSS	Dnd41	blood
6	chr17:46047400-46048400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:46047400-46049200	Active TSS	Fetal Kidney	kidney
8	chr17:46047600-46048200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:46047600-46048200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:46047600-46048200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr17:46047600-46048200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr17:46047600-46048200	Flanking Active TSS	Primary B cells from peripheral blood	blood
13	chr17:46047600-46048200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr17:46047600-46048200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr17:46047600-46048200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr17:46047600-46048200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr17:46047600-46048200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr17:46047600-46048200	Flanking Active TSS	Liver	Liver
19	chr17:46047600-46048200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr17:46047600-46048200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr17:46047600-46048200	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr17:46047600-46048200	Flanking Active TSS	A549	lung
23	chr17:46047600-46048200	Flanking Active TSS	K562	blood
24	chr17:46047600-46048200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr17:46047600-46049400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:46047600-46049600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:46047800-46048200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr17:46047800-46048200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:46047800-46048200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr17:46047800-46048200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:46047800-46048200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr17:46047800-46048200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr17:46047800-46048200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr17:46047800-46048200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:46047800-46048200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:46047800-46048200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:46047800-46048200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr17:46047800-46048200	Flanking Active TSS	Fetal Heart	heart
39	chr17:46047800-46048200	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr17:46047800-46048200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr17:46047800-46048200	Flanking Active TSS	Fetal Stomach	stomach
42	chr17:46047800-46048200	Flanking Active TSS	Fetal Thymus	thymus
43	chr17:46047800-46048200	Flanking Active TSS	Pancreas	Pancrea
44	chr17:46047800-46048200	Flanking Active TSS	Thymus	Thymus
45	chr17:46047800-46048200	Flanking Active TSS	Hela-S3	cervix
46	chr17:46047800-46048200	Flanking Active TSS	HMEC	breast
47	chr17:46047800-46048200	Flanking Active TSS	HUVEC	blood vessel
48	chr17:46047800-46048200	Flanking Active TSS	NHEK	skin
49	chr17:46047800-46048200	Flanking Active TSS	Osteobl	bone
50	chr17:46047800-46048800	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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