Variant report

Variant	rs375638786
Chromosome Location	chr17:20058939-20058940
allele	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	MAX	chr17:20058798-20060196	ECC-1	luminal epithelium:	n/a	chr17:20059908-20059918
2	POLR2A	chr17:20058906-20060030	K562	blood:	n/a	n/a
3	EP300	chr17:20058865-20059172	GM12878	blood:	n/a	n/a
4	UBTF	chr17:20058903-20060154	K562	blood:	n/a	n/a
5	ELF1	chr17:20058892-20059394	MCF-7	breast:	n/a	n/a
6	POU2F2	chr17:20058806-20059502	GM12891	blood:	n/a	chr17:20058826-20058839
7	MAFK	chr17:20058658-20059822	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:20058939-20060092	Hela-S3	cervix:	n/a	n/a
9	TCF12	chr17:20058921-20059415	GM12878	blood:	n/a	n/a
10	ZNF143	chr17:20058926-20059452	GM12878	blood:	n/a	chr17:20059105-20059115
11	POLR2A	chr17:20058248-20060182	GM19099	blood:	n/a	n/a
12	RUNX3	chr17:20058405-20060038	GM12878	blood:	n/a	n/a
13	BCL3	chr17:20058724-20059784	A549	lung:	n/a	n/a
14	BACH1	chr17:20058917-20059433	H1-hESC	embryonic stem cell:	n/a	n/a
15	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
16	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
17	USF1	chr17:20058865-20059582	A549	lung:	n/a	chr17:20059224-20059240
18	POLR2A	chr17:20058769-20059543	GM12892	blood:	n/a	n/a
19	PAX5	chr17:20058864-20059243	GM12891	blood:	n/a	n/a
20	CHD2	chr17:20058926-20059798	GM12878	blood:	n/a	chr17:20059278-20059288 chr17:20059216-20059226
21	NFATC1	chr17:20058583-20059313	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:20058932-20059646	K562	blood:	n/a	n/a
23	POLR2A	chr17:20058922-20059771	U87	brain:	n/a	n/a
24	SIN3AK20	chr17:20058908-20059183	A549	lung:	n/a	n/a
25	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
26	POLR2A	chr17:20058864-20060068	MCF-7	breast:	n/a	n/a
27	MXI1	chr17:20058795-20059495	K562	blood:	n/a	n/a
28	MAFK	chr17:20058774-20059222	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr17:20058893-20060266	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr17:20058773-20059189	GM12891	blood:	n/a	n/a
31	PBX3	chr17:20058904-20059446	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr17:20058836-20060094	H1-hESC	embryonic stem cell:	n/a	n/a
33	PAX5	chr17:20058791-20059365	GM12878	blood:	n/a	n/a
34	ELK1	chr17:20058546-20059259	GM12878	blood:	n/a	n/a
35	FOXM1	chr17:20058379-20059387	GM12878	blood:	n/a	n/a
36	SIN3AK20	chr17:20058694-20060740	MCF-7	breast:	n/a	n/a
37	POLR2A	chr17:20058523-20060050	GM18951	blood:	n/a	n/a
38	MAX	chr17:20058826-20059553	MCF-7	breast:	n/a	n/a
39	NFIC	chr17:20058371-20059414	GM12878	blood:	n/a	n/a
40	TAF1	chr17:20058896-20059608	H1-neurons	neurons:	n/a	n/a
41	RELA	chr17:20057945-20059382	GM18505	blood:	n/a	n/a
42	MAX	chr17:20058825-20060314	A549	lung:	n/a	chr17:20059908-20059918
43	RELA	chr17:20058609-20059392	GM18951	blood:	n/a	n/a
44	POLR2A	chr17:20058916-20060659	Hela-S3	cervix:	n/a	n/a
45	EP300	chr17:20058528-20059223	GM12878	blood:	n/a	n/a
46	CEBPB	chr17:20058910-20060106	HCT-116	colon:	n/a	chr17:20059704-20059715 chr17:20059703-20059714
47	MTA3	chr17:20058345-20059378	GM12878	blood:	n/a	n/a
48	USF2	chr17:20058862-20059191	Hela-S3	cervix:	n/a	n/a
49	RCOR1	chr17:20058910-20060253	K562	blood:	n/a	n/a
50	EGR1	chr17:20058881-20059502	H1-hESC	embryonic stem cell:	n/a	chr17:20059211-20059225 chr17:20059285-20059298 chr17:20059140-20059153 chr17:20059138-20059148 chr17:20059213-20059222

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
ENSG00000232671	Chromatin interaction
ENSG00000108599	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000128487	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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20057000-20059000	Weak transcription	Colonic Mucosa	Colon
2	chr17:20058000-20059000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:20058000-20059000	Enhancers	Fetal Heart	heart
4	chr17:20058200-20059000	Weak transcription	Spleen	Spleen
5	chr17:20058400-20059000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr17:20058400-20059000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr17:20058400-20059000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr17:20058400-20059000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr17:20058400-20059000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:20058400-20059000	Flanking Active TSS	GM12878-XiMat	blood
11	chr17:20058400-20059200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr17:20058400-20060000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr17:20058400-20060200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr17:20058600-20059000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
15	chr17:20058600-20059000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr17:20058600-20059000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:20058600-20059000	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr17:20058600-20059000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:20058600-20059000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr17:20058600-20059000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:20058600-20059000	Flanking Active TSS	A549	lung
22	chr17:20058600-20059000	Flanking Active TSS	NHEK	skin
23	chr17:20058600-20059200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr17:20058600-20059200	Flanking Active TSS	HMEC	breast
25	chr17:20058600-20059400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:20058600-20059600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:20058600-20060000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr17:20058600-20060200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:20058600-20060400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:20058600-20060400	Active TSS	Duodenum Mucosa	Duodenum
31	chr17:20058800-20059000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr17:20058800-20059000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:20058800-20059000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:20058800-20059000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:20058800-20059000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr17:20058800-20059000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr17:20058800-20059000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr17:20058800-20059000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:20058800-20059000	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr17:20058800-20059000	Active TSS	Primary T cells fromperipheralblood	blood
41	chr17:20058800-20059000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr17:20058800-20059000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr17:20058800-20059000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr17:20058800-20059000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:20058800-20059000	Enhancers	Liver	Liver
46	chr17:20058800-20059000	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr17:20058800-20059000	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr17:20058800-20059000	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr17:20058800-20059000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr17:20058800-20059000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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