Variant report

Variant	rs56180580
Chromosome Location	chr17:18280963-18280964
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	chr17:18280638-18281170	NB4	blood:	n/a	chr17:18281123-18281133
2	POLR2A	chr17:18280593-18281318	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr17:18280919-18281163	HepG2	liver:	n/a	n/a
4	TBP	chr17:18280692-18281180	Hela-S3	cervix:	n/a	n/a
5	MAX	chr17:18280717-18281300	MCF-7	breast:	n/a	chr17:18281123-18281133
6	ZKSCAN1	chr17:18280665-18281250	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr17:18280716-18281520	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr17:18280845-18281055	IMR90	lung:	n/a	chr17:18280955-18280966
9	HDAC2	chr17:18280696-18281118	MCF-7	breast:	n/a	n/a
10	USF2	chr17:18280785-18281077	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr17:18280704-18281187	HL-60	blood:	n/a	n/a
12	RCOR1	chr17:18280724-18281397	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr17:18280781-18281159	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr17:18280595-18281453	MCF-7	breast:	n/a	chr17:18281161-18281169 chr17:18280832-18280840
15	CEBPB	chr17:18280669-18281257	MCF-7	breast:	n/a	chr17:18280955-18280966
16	STAT3	chr17:18280837-18281092	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr17:18280774-18281128	MCF10A-Er-Src	breast:	n/a	chr17:18280971-18280978
18	BHLHE40	chr17:18280957-18281131	GM12878	blood:	n/a	n/a
19	MAFK	chr17:18280838-18281170	Hela-S3	cervix:	n/a	n/a
20	MAX	chr17:18280614-18281182	Hela-S3	cervix:	n/a	chr17:18281123-18281133
21	POLR2A	chr17:18280658-18281209	MCF-7	breast:	n/a	n/a
22	POLR2A	chr17:18280757-18281211	MCF10A-Er-Src	breast:	n/a	n/a
23	FOXA1	chr17:18280606-18281102	T-47D	breast:	n/a	n/a
24	POLR2A	chr17:18280602-18281664	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr17:18280754-18281501	Hela-S3	cervix:	n/a	chr17:18281395-18281408 chr17:18281366-18281380
26	GATA3	chr17:18280612-18281157	T-47D	breast:	n/a	chr17:18280832-18280840
27	MAX	chr17:18280593-18281609	MCF-7	breast:	n/a	chr17:18281123-18281133
28	POLR2A	chr17:18280587-18281478	MCF-7	breast:	n/a	n/a
29	SMARCB1	chr17:18280656-18281620	Hela-S3	cervix:	n/a	n/a
30	MAX	chr17:18280672-18281559	Hela-S3	cervix:	n/a	chr17:18281123-18281133
31	TAF1	chr17:18280714-18280975	Hela-S3	cervix:	n/a	n/a
32	GTF2F1	chr17:18280727-18281193	Hela-S3	cervix:	n/a	n/a
33	GATA3	chr17:18280522-18281128	MCF-7	breast:	n/a	chr17:18280832-18280840
34	CEBPB	chr17:18280691-18281529	Hela-S3	cervix:	n/a	chr17:18280955-18280966
35	ELK1	chr17:18280790-18281040	Hela-S3	cervix:	n/a	n/a
36	EP300	chr17:18280699-18281250	T-47D	breast:	n/a	chr17:18280706-18280722
37	MAZ	chr17:18280683-18281650	Hela-S3	cervix:	n/a	chr17:18281123-18281133
38	CEBPB	chr17:18280773-18281113	HepG2	liver:	n/a	chr17:18280955-18280966
39	STAT3	chr17:18280888-18281107	MCF10A-Er-Src	breast:	n/a	n/a
40	CEBPB	chr17:18280775-18281332	HepG2	liver:	n/a	chr17:18280955-18280966
41	MYC	chr17:18280775-18281003	MCF-7	breast:	n/a	n/a
42	CEBPB	chr17:18280887-18280990	K562	blood:	n/a	chr17:18280955-18280966
43	EP300	chr17:18280600-18281166	T-47D	breast:	n/a	chr17:18280706-18280722
44	POLR2A	chr17:18280822-18281065	HepG2	liver:	n/a	n/a
45	MXI1	chr17:18280726-18281167	Hela-S3	cervix:	n/a	chr17:18281134-18281143
46	GATA3	chr17:18280598-18281157	T-47D	breast:	n/a	chr17:18280832-18280840
47	POLR2A	chr17:18280657-18281180	HL-60	blood:	n/a	n/a
48	FOXA1	chr17:18280660-18281018	T-47D	breast:	n/a	n/a
49	CEBPB	chr17:18280844-18281067	HepG2	liver:	n/a	chr17:18280955-18280966
50	POLR2A	chr17:18280698-18281397	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18160932..18162896-chr17:18279447..18281125,2	MCF-7	breast:
2	chr13:111365369..111366036-chr17:18280882..18281427,2	Hela-S3	cervix:

Variant related genes	Relation type
EVPLL	TF binding region
ENSG00000177731	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs28694704	1.00[EUR][1000 genomes]
rs56109231	1.00[EUR][1000 genomes]
rs56735648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56793258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58115308	1.00[EUR][1000 genomes]
rs58499955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59738176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59867698	1.00[EUR][1000 genomes]
rs60320587	1.00[EUR][1000 genomes]
rs60510653	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60699593	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60708953	1.00[EUR][1000 genomes]
rs60814048	1.00[EUR][1000 genomes]
rs61361031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61576260	1.00[EUR][1000 genomes]
rs7207131	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207489	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213472	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213789	1.00[EUR][1000 genomes]
rs7219191	1.00[EUR][1000 genomes]
rs7226015	1.00[EUR][1000 genomes]
rs73288279	1.00[EUR][1000 genomes]
rs73288297	1.00[EUR][1000 genomes]
rs73288302	1.00[EUR][1000 genomes]
rs73289913	1.00[EUR][1000 genomes]
rs8064901	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068530	1.00[EUR][1000 genomes]
rs8069012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8071028	1.00[EUR][1000 genomes]
rs8071911	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8074322	1.00[EUR][1000 genomes]
rs8080816	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910599	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
12	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
14	nsv978378	chr17:18272529-18321736	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv962275	chr17:18272529-18471923	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
16	nsv833388	chr17:18275146-18454773	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
17	nsv907778	chr17:18275847-18409309	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv469661	chr17:18275972-18446377	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
19	nsv482696	chr17:18275972-18446377	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
20	nsv827914	chr17:18278173-18424843	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1058895	chr17:18278477-18474634	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18267200-18288200	Weak transcription	Right Atrium	heart
2	chr17:18277800-18281000	Weak transcription	A549	lung
3	chr17:18279800-18281400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr17:18279800-18281400	Enhancers	Spleen	Spleen
5	chr17:18279800-18281800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr17:18280200-18281000	Enhancers	NHEK	skin
7	chr17:18280400-18281600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr17:18280400-18281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:18280400-18284200	Enhancers	Stomach Mucosa	stomach
10	chr17:18280600-18281000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:18280600-18281200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:18280600-18281200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:18280600-18281200	Flanking Active TSS	HepG2	liver
14	chr17:18280600-18281400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr17:18280600-18281400	Enhancers	Fetal Intestine Small	intestine
16	chr17:18280600-18281400	Enhancers	Fetal Thymus	thymus
17	chr17:18280600-18281400	Enhancers	Gastric	stomach
18	chr17:18280600-18281400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr17:18280600-18281400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr17:18280600-18281400	Enhancers	Thymus	Thymus
21	chr17:18280600-18281400	Enhancers	GM12878-XiMat	blood
22	chr17:18280600-18281400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr17:18280600-18281600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr17:18280600-18281600	Enhancers	Primary B cells from cord blood	blood
25	chr17:18280600-18281600	Enhancers	Primary hematopoietic stem cells	blood
26	chr17:18280600-18281600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:18280600-18281600	Enhancers	Colonic Mucosa	Colon
28	chr17:18280600-18281600	Enhancers	Fetal Stomach	stomach
29	chr17:18280600-18281600	Enhancers	HMEC	breast
30	chr17:18280600-18281800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:18280600-18281800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr17:18280600-18281800	Enhancers	Primary B cells from peripheral blood	blood
33	chr17:18280600-18281800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:18280600-18281800	Enhancers	Liver	Liver
35	chr17:18280600-18282000	Enhancers	Adipose Nuclei	Adipose
36	chr17:18280600-18282000	Enhancers	Duodenum Mucosa	Duodenum
37	chr17:18280600-18283200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr17:18280600-18283800	Enhancers	Placenta	Placenta
39	chr17:18280800-18281000	Active TSS	Hela-S3	cervix
40	chr17:18280800-18281200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr17:18280800-18281400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr17:18280800-18281600	Enhancers	Fetal Intestine Large	intestine
43	chr17:18280800-18281800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:18280800-18282000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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