Variant report

Variant	rs598292
Chromosome Location	chr1:241804805-241804806
allele	A/C
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	EP300	chr1:241803745-241806107	A549	lung:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241803841-241803857 chr1:241804622-241804636
2	NR3C1	chr1:241804385-241804945	A549	lung:	n/a	n/a
3	NR3C1	chr1:241804320-241804907	A549	lung:	n/a	n/a
4	MAX	chr1:241803269-241805364	A549	lung:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
5	JUND	chr1:241803958-241805583	Hela-S3	cervix:	n/a	chr1:241805169-241805180
6	BCL3	chr1:241803712-241804889	A549	lung:	n/a	n/a
7	MAX	chr1:241803199-241805449	Hela-S3	cervix:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
8	RPC155	chr1:241804694-241805774	Hela-S3	cervix:	n/a	n/a
9	FOSL2	chr1:241803746-241805666	A549	lung:	n/a	n/a
10	CHD2	chr1:241803105-241805505	Hela-S3	cervix:	n/a	chr1:241803837-241803847
11	JUN	chr1:241804122-241805483	Hela-S3	cervix:	n/a	n/a
12	MAFK	chr1:241803857-241805405	Hela-S3	cervix:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
13	TBP	chr1:241803265-241804928	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:241802347-241805302	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr1:241804030-241805438	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
16	CEBPB	chr1:241803232-241805865	Hela-S3	cervix:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
17	MXI1	chr1:241803216-241805469	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr1:241804066-241805453	Hela-S3	cervix:	n/a	n/a
19	HEY1	chr1:241804469-241804849	HepG2	liver:	n/a	n/a
20	SP1	chr1:241803416-241806004	A549	lung:	n/a	chr1:241803838-241803852 chr1:241803942-241803956 chr1:241803838-241803848 chr1:241803839-241803848 chr1:241803837-241803849 chr1:241803707-241803718 chr1:241803838-241803847 chr1:241803740-241803751 chr1:241803838-241803848 chr1:241803696-241803707 chr1:241803838-241803847 chr1:241803837-241803849
21	ELK1	chr1:241803629-241805441	Hela-S3	cervix:	n/a	n/a
22	TAF1	chr1:241804440-241804943	Hela-S3	cervix:	n/a	n/a
23	FOS	chr1:241803948-241805396	Hela-S3	cervix:	n/a	chr1:241805169-241805180
24	FOXA2	chr1:241804413-241804907	A549	lung:	n/a	n/a
25	E2F6	chr1:241803579-241805120	A549	lung:	n/a	chr1:241803839-241803848 chr1:241804035-241804044
26	EP300	chr1:241804568-241805418	HepG2	liver:	n/a	chr1:241804622-241804636
27	POLR2A	chr1:241804278-241804964	Hela-S3	cervix:	n/a	n/a
28	TFAP2C	chr1:241803198-241805402	Hela-S3	cervix:	n/a	chr1:241803895-241803910
29	BCL3	chr1:241804258-241805505	A549	lung:	n/a	n/a
30	SMC3	chr1:241803172-241805588	Hela-S3	cervix:	n/a	n/a
31	FOS	chr1:241804418-241805407	MCF10A-Er-Src	breast:	n/a	chr1:241805169-241805180
32	FOS	chr1:241804392-241805437	MCF10A-Er-Src	breast:	n/a	chr1:241805169-241805180
33	MAFK	chr1:241804107-241805353	HepG2	liver:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
34	STAT3	chr1:241804011-241805462	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
35	CEBPB	chr1:241804433-241804825	K562	blood:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
36	POLR2A	chr1:241801599-241805416	Hela-S3	cervix:	n/a	n/a
37	MYBL2	chr1:241804394-241805533	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:241802932-241804993	HepG2	liver:	n/a	n/a
39	ARID3A	chr1:241804647-241805695	HepG2	liver:	n/a	n/a
40	CEBPB	chr1:241804401-241804949	A549	lung:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
41	POLR2A	chr1:241802948-241804992	HepG2	liver:	n/a	n/a
42	ELK4	chr1:241803831-241804905	Hela-S3	cervix:	n/a	n/a
43	CREB1	chr1:241804376-241804958	A549	lung:	n/a	n/a
44	SMARCB1	chr1:241802469-241805865	Hela-S3	cervix:	n/a	n/a
45	MAX	chr1:241803261-241804856	HepG2	liver:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
46	E2F6	chr1:241802834-241804931	K562	blood:	n/a	chr1:241803839-241803848 chr1:241802963-241802975 chr1:241804035-241804044
47	ZKSCAN1	chr1:241803221-241805470	Hela-S3	cervix:	n/a	chr1:241803891-241803904 chr1:241803825-241803838
48	EP300	chr1:241804012-241805414	Hela-S3	cervix:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241804622-241804636
49	POLR2A	chr1:241803096-241805032	Hela-S3	cervix:	n/a	n/a
50	NFYB	chr1:241804336-241804985	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241804722..241806985-chr1:241808766..241812200,3	MCF-7	breast:
2	chr1:241693526..241696085-chr1:241801417..241805051,3	MCF-7	breast:
3	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
4	chr1:241801200..241805205-chr1:241910998..241914529,7	MCF-7	breast:
5	chr1:241802310..241805173-chr1:241993132..241995327,2	K562	blood:
6	chr1:241804081..241806043-chr1:241997998..241999955,2	MCF-7	breast:
7	chr1:241796724..241805103-chr1:242008052..242013159,15	K562	blood:
8	chr1:241799658..241805161-chr1:242010004..242013743,14	K562	blood:
9	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
10	chr1:241801957..241807032-chr1:241808533..241817679,11	K562	blood:

Variant related genes	Relation type
OPN3	TF binding region
ENSG00000229022	Chromatin interaction
ENSG00000117009	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000162843	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12072899	1.00[MEX][hapmap]
rs2784165	0.93[ASW][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.91[AFR][1000 genomes]
rs595397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs610693	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613797	0.93[ASW][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];0.94[AFR][1000 genomes]
rs615141	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs616020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626437	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs626443	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs629088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs630879	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs643321	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9428514	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS 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	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	esv3399692	chr1:241802554-241805102	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241803800-241806200	Flanking Active TSS	Hela-S3	cervix
2	chr1:241804000-241805000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:241804000-241805600	Flanking Active TSS	HepG2	liver
4	chr1:241804000-241806200	Flanking Active TSS	A549	lung
5	chr1:241804200-241805000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:241804200-241805000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:241804200-241805000	Enhancers	HMEC	breast
8	chr1:241804200-241805000	ZNF genes & repeats	K562	blood
9	chr1:241804200-241805000	Enhancers	NH-A	brain
10	chr1:241804200-241805200	Weak transcription	Liver	Liver
11	chr1:241804200-241805400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:241804200-241805400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:241804200-241805400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:241804200-241805600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:241804200-241805600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:241804200-241805600	Enhancers	Stomach Mucosa	stomach
17	chr1:241804200-241805600	Enhancers	HUVEC	blood vessel
18	chr1:241804200-241805600	Enhancers	NHDF-Ad	bronchial
19	chr1:241804200-241805600	Enhancers	Osteobl	bone
20	chr1:241804200-241805800	Enhancers	Placenta	Placenta
21	chr1:241804200-241805800	Enhancers	NHEK	skin
22	chr1:241804200-241806800	Enhancers	Fetal Intestine Large	intestine
23	chr1:241804200-241808600	Weak transcription	Ovary	ovary
24	chr1:241804200-241809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:241804400-241805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:241804400-241805800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:241804400-241809400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:241804400-241809600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:241804600-241805000	Enhancers	Lung	lung
30	chr1:241804600-241805400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:241804600-241805600	Enhancers	NHLF	lung
32	chr1:241804800-241805000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:241804800-241805000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:241804800-241805000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:241804800-241808600	Weak transcription	Gastric	stomach

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