Variant report

Variant	rs140828285
Chromosome Location	chr17:20059054-20059055
allele	C/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	chr17:20058798-20060196	ECC-1	luminal epithelium:	n/a	chr17:20059908-20059918
2	E2F4	chr17:20058966-20059714	MCF10A-Er-Src	breast:	n/a	chr17:20059277-20059286 chr17:20059329-20059340 chr17:20059215-20059224
3	POLR2A	chr17:20058906-20060030	K562	blood:	n/a	n/a
4	EGR1	chr17:20059009-20059361	GM12878	blood:	n/a	chr17:20059211-20059225 chr17:20059285-20059298 chr17:20059140-20059153 chr17:20059138-20059148 chr17:20059213-20059222
5	CCNT2	chr17:20058984-20060125	K562	blood:	n/a	chr17:20059587-20059596
6	EP300	chr17:20058865-20059172	GM12878	blood:	n/a	n/a
7	UBTF	chr17:20058903-20060154	K562	blood:	n/a	n/a
8	JUND	chr17:20059016-20059347	H1-hESC	embryonic stem cell:	n/a	n/a
9	ELF1	chr17:20058892-20059394	MCF-7	breast:	n/a	n/a
10	POU2F2	chr17:20058806-20059502	GM12891	blood:	n/a	chr17:20058826-20058839
11	MAFK	chr17:20058658-20059822	Hela-S3	cervix:	n/a	n/a
12	FOXA1	chr17:20058963-20059451	T-47D	breast:	n/a	n/a
13	POLR2A	chr17:20058939-20060092	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr17:20058921-20059415	GM12878	blood:	n/a	n/a
15	ZNF143	chr17:20058926-20059452	GM12878	blood:	n/a	chr17:20059105-20059115
16	MYC	chr17:20058978-20059343	MCF-7	breast:	n/a	n/a
17	POLR2A	chr17:20058248-20060182	GM19099	blood:	n/a	n/a
18	POLR2A	chr17:20058990-20059057	ProgFib	skin:	n/a	n/a
19	RUNX3	chr17:20058405-20060038	GM12878	blood:	n/a	n/a
20	MAX	chr17:20059050-20059649	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:20058945-20059522	SK-N-SH	brain:	n/a	n/a
22	BCL3	chr17:20058724-20059784	A549	lung:	n/a	n/a
23	BACH1	chr17:20058917-20059433	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr17:20058966-20059678	A549	lung:	n/a	n/a
25	GTF2F1	chr17:20058970-20059697	H1-hESC	embryonic stem cell:	n/a	n/a
26	MEF2C	chr17:20058541-20059408	GM12878	blood:	n/a	chr17:20058830-20058851 chr17:20058681-20058696 chr17:20058834-20058845 chr17:20058679-20058696 chr17:20058832-20058847 chr17:20058831-20058847
27	FOS	chr17:20059005-20059272	MCF10A-Er-Src	breast:	n/a	n/a
28	SP1	chr17:20058436-20059381	GM12878	blood:	n/a	chr17:20059276-20059288 chr17:20059214-20059226 chr17:20059276-20059288 chr17:20059214-20059226 chr17:20059216-20059225 chr17:20059277-20059286 chr17:20059278-20059287 chr17:20059137-20059149 chr17:20059215-20059224
29	USF1	chr17:20058865-20059582	A549	lung:	n/a	chr17:20059224-20059240
30	POLR2A	chr17:20058769-20059543	GM12892	blood:	n/a	n/a
31	ZMIZ1	chr17:20058987-20059527	K562	blood:	n/a	n/a
32	MAX	chr17:20059029-20060271	K562	blood:	n/a	chr17:20059908-20059918
33	PAX5	chr17:20058864-20059243	GM12891	blood:	n/a	n/a
34	CHD2	chr17:20058926-20059798	GM12878	blood:	n/a	chr17:20059278-20059288 chr17:20059216-20059226
35	POLR2A	chr17:20059000-20059267	HCT-116	colon:	n/a	n/a
36	TAF1	chr17:20058955-20059535	K562	blood:	n/a	n/a
37	NFATC1	chr17:20058583-20059313	GM12878	blood:	n/a	n/a
38	MXI1	chr17:20059040-20059708	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr17:20058976-20060152	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr17:20058932-20059646	K562	blood:	n/a	n/a
41	MYC	chr17:20059001-20059608	MCF-7	breast:	n/a	n/a
42	POLR2A	chr17:20058922-20059771	U87	brain:	n/a	n/a
43	YY1	chr17:20059037-20059172	K562	blood:	n/a	n/a
44	SIN3AK20	chr17:20058908-20059183	A549	lung:	n/a	n/a
45	MEF2A	chr17:20058397-20059342	GM12878	blood:	n/a	chr17:20058830-20058851 chr17:20058681-20058696 chr17:20058834-20058845 chr17:20058679-20058696 chr17:20058832-20058847 chr17:20058831-20058847
46	POLR2A	chr17:20058864-20060068	MCF-7	breast:	n/a	n/a
47	MXI1	chr17:20058795-20059495	K562	blood:	n/a	n/a
48	MAFK	chr17:20058774-20059222	H1-hESC	embryonic stem cell:	n/a	n/a
49	TAF1	chr17:20058893-20060266	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr17:20058990-20060436	IMR90	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:20059054-20059104	HUVEC	blood vessel:	n/a
2	chr17:20059029-20059079	HEEpiC	esophagus:	n/a
3	chr17:20059029-20059079	ProgFib	skin:	n/a
4	chr17:20059054-20059104	Caco-2	colon:	n/a
5	chr17:20059054-20059104	HCT-116	colon:	n/a
6	chr17:20059054-20059104	RPTEC	kidney:	n/a
7	chr17:20059054-20059104	HIPEpiC	eye:	n/a
8	chr17:20059054-20059104	BE2_C	brain:	n/a
9	chr17:20059054-20059104	HCF	heart:	n/a
10	chr17:20059054-20059104	MCF-7	breast:	n/a
11	chr17:20059054-20059104	HCPEpiC	choroid plexus:	n/a
12	chr17:20059054-20059104	U87	brain:	n/a
13	chr17:20059054-20059104	HRCEpiC	kidney:	n/a
14	chr17:20059029-20059079	CMK	blood:	n/a
15	chr17:20059029-20059079	SK-N-MC	brain:	n/a
16	chr17:20059054-20059104	CMK	blood:	n/a
17	chr17:20059054-20059104	ECC-1	luminal epithelium:	n/a
18	chr17:20059054-20059104	SK-N-SH	brain:	n/a
19	chr17:20059054-20059104	GM12878	blood:	n/a
20	chr17:20059054-20059104	NH-A	brain:	n/a
21	chr17:20059054-20059104	HPAEpiC	pulmonary alveolar:	n/a
22	chr17:20059029-20059079	AG09309	skin:	n/a
23	chr17:20059029-20059079	IMR90	lung:	fetal
24	chr17:20059054-20059104	ovcar-3	ovarian:	n/a
25	chr17:20059029-20059079	HRCEpiC	kidney:	n/a
26	chr17:20059029-20059079	HCT-116	colon:	n/a
27	chr17:20059029-20059079	PFSK-1	brain:	n/a
28	chr17:20059054-20059104	NB4	blood:	n/a
29	chr17:20059054-20059104	GM19239	blood:	n/a
30	chr17:20059054-20059104	T-47D	breast:	n/a
31	chr17:20059029-20059079	NHDF-neo	bronchial:	n/a
32	chr17:20059029-20059079	AG09319	gingival:	n/a
33	chr17:20059029-20059079	HIPEpiC	eye:	n/a
34	chr17:20059029-20059079	BJ	skin:	n/a
35	chr17:20059029-20059079	Hepatocyte	liver:	n/a
36	chr17:20059029-20059079	NB4	blood:	n/a
37	chr17:20059029-20059079	HepG2	liver:	n/a
38	chr17:20059054-20059104	Hela-S3	cervix:	n/a
39	chr17:20059054-20059104	Jurkat	blood:	n/a
40	chr17:20059054-20059104	SKMC	muscle:	n/a
41	chr17:20059029-20059079	NH-A	brain:	n/a
42	chr17:20059029-20059079	AG10803	skin:	n/a
43	chr17:20059054-20059104	HMEC	breast:	n/a
44	chr17:20059029-20059079	PANC-1	pancreas:	n/a
45	chr17:20059029-20059079	GM12892	blood:	n/a
46	chr17:20059054-20059104	HEEpiC	esophagus:	n/a
47	chr17:20059029-20059079	K562	blood:	n/a
48	chr17:20059029-20059079	GM19239	blood:	n/a
49	chr17:20059054-20059104	PrEC	prostate:	n/a
50	chr17:20059054-20059104	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:20058693..20060833-chr17:20107962..20111201,3	MCF-7	breast:
2	chr1:151253915..151254758-chr17:20058799..20059680,2	Hela-S3	cervix:
3	chr17:20057192..20060270-chr17:20108096..20110844,3	K562	blood:
4	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:

Variant related genes	Relation type
SPECC1	TF binding region
SPECC1	CpG island
ENSG00000108599	Chromatin interaction
ENSG00000128487	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	esv3314150	chr17:20058385-20061233	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv3314151	chr17:20058385-20061233	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20058400-20059200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr17:20058400-20060000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
3	chr17:20058400-20060200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr17:20058600-20059200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr17:20058600-20059200	Flanking Active TSS	HMEC	breast
6	chr17:20058600-20059400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:20058600-20059600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:20058600-20060000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr17:20058600-20060200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:20058600-20060400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:20058600-20060400	Active TSS	Duodenum Mucosa	Duodenum
12	chr17:20058800-20059200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:20058800-20059200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:20058800-20059200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:20058800-20059200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr17:20058800-20059200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:20058800-20059200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr17:20058800-20059200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:20058800-20059200	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr17:20058800-20059200	Bivalent/Poised TSS	Fetal Brain Male	brain
21	chr17:20058800-20059200	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr17:20058800-20059200	Flanking Active TSS	Placenta	Placenta
23	chr17:20058800-20059200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr17:20058800-20059200	Flanking Bivalent TSS/Enh	Dnd41	blood
25	chr17:20058800-20059200	Flanking Active TSS	Hela-S3	cervix
26	chr17:20058800-20059200	Flanking Active TSS	HUVEC	blood vessel
27	chr17:20058800-20059600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:20058800-20059600	Active TSS	Left Ventricle	heart
29	chr17:20058800-20059800	Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr17:20058800-20059800	Active TSS	Right Ventricle	heart
31	chr17:20058800-20059800	Active TSS	NHLF	lung
32	chr17:20058800-20060000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:20058800-20060000	Active TSS	Colon Smooth Muscle	Colon
34	chr17:20058800-20060000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
35	chr17:20058800-20060000	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr17:20058800-20060200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:20058800-20060200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:20058800-20060200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:20058800-20060200	Active TSS	Primary T cells from cord blood	blood
40	chr17:20058800-20060200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:20058800-20060200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr17:20058800-20060200	Active TSS	Fetal Intestine Large	intestine
43	chr17:20058800-20060200	Active TSS	Fetal Intestine Small	intestine
44	chr17:20058800-20060200	Active TSS	Rectal Smooth Muscle	rectum
45	chr17:20058800-20060200	Active TSS	Osteobl	bone
46	chr17:20058800-20060400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr17:20058800-20060400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:20058800-20060400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:20058800-20060400	Active TSS	Aorta	Aorta
50	chr17:20058800-20060400	Active TSS	Esophagus	oesophagus

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