Variant report

Variant	rs643321
Chromosome Location	chr1:241805206-241805207
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	FOXA2	chr1:241804952-241805554	A549	lung:	n/a	n/a
2	EP300	chr1:241803745-241806107	A549	lung:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241803841-241803857 chr1:241804622-241804636
3	CBX3	chr1:241805065-241806293	K562	blood:	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	MAX	chr1:241803199-241805449	Hela-S3	cervix:	n/a	chr1:241804047-241804056 chr1:241803840-241803850 chr1:241804048-241804055 chr1:241804047-241804056 chr1:241804047-241804057
7	RPC155	chr1:241804694-241805774	Hela-S3	cervix:	n/a	n/a
8	FOSL2	chr1:241803746-241805666	A549	lung:	n/a	n/a
9	CHD2	chr1:241803105-241805505	Hela-S3	cervix:	n/a	chr1:241803837-241803847
10	JUN	chr1:241804122-241805483	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr1:241803857-241805405	Hela-S3	cervix:	n/a	chr1:241804877-241804892 chr1:241805164-241805179
12	TEAD4	chr1:241804997-241805487	A549	lung:	n/a	n/a
13	FOXA1	chr1:241805104-241805334	T-47D	breast:	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	EP300	chr1:241805008-241805345	HepG2	liver:	n/a	n/a
17	CEBPB	chr1:241803232-241805865	Hela-S3	cervix:	n/a	chr1:241804623-241804634 chr1:241804621-241804632 chr1:241804621-241804634 chr1:241804623-241804632
18	MXI1	chr1:241803216-241805469	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr1:241804066-241805453	Hela-S3	cervix:	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	SRF	chr1:241805018-241805293	HepG2	liver:	n/a	n/a
23	FOS	chr1:241803948-241805396	Hela-S3	cervix:	n/a	chr1:241805169-241805180
24	FOSL2	chr1:241804994-241805361	A549	lung:	n/a	n/a
25	JUND	chr1:241805053-241805395	HepG2	liver:	n/a	chr1:241805169-241805180
26	EP300	chr1:241804568-241805418	HepG2	liver:	n/a	chr1:241804622-241804636
27	FOXA1	chr1:241805066-241805357	HepG2	liver:	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	SRF	chr1:241805052-241805320	HepG2	liver:	n/a	n/a
35	STAT3	chr1:241804011-241805462	MCF10A-Er-Src	breast:	n/a	chr1:241804179-241804199 chr1:241804951-241804958
36	POLR2A	chr1:241801599-241805416	Hela-S3	cervix:	n/a	n/a
37	FOXA2	chr1:241805058-241805566	A549	lung:	n/a	n/a
38	MYBL2	chr1:241804394-241805533	HepG2	liver:	n/a	n/a
39	ARID3A	chr1:241804647-241805695	HepG2	liver:	n/a	n/a
40	NR3C1	chr1:241805075-241805454	A549	lung:	n/a	n/a
41	CREB1	chr1:241805186-241805457	A549	lung:	n/a	n/a
42	FOSL2	chr1:241805002-241805411	HepG2	liver:	n/a	n/a
43	SMARCB1	chr1:241802469-241805865	Hela-S3	cervix:	n/a	n/a
44	MAFF	chr1:241805042-241805304	K562	blood:	n/a	n/a
45	ZKSCAN1	chr1:241803221-241805470	Hela-S3	cervix:	n/a	chr1:241803891-241803904 chr1:241803825-241803838
46	EP300	chr1:241804012-241805414	Hela-S3	cervix:	n/a	chr1:241804139-241804149 chr1:241804154-241804164 chr1:241804622-241804636
47	NFYA	chr1:241804306-241805380	Hela-S3	cervix:	n/a	n/a
48	MAFF	chr1:241805026-241805395	HepG2	liver:	n/a	n/a
49	GATA3	chr1:241803487-241805601	A549	lung:	n/a	n/a
50	USF2	chr1:241803864-241805842	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	chr1:241799844..241805446-chr1:241909864..241915090,9	MCF-7	breast:
3	chr1:241804081..241806043-chr1:241997998..241999955,2	MCF-7	breast:
4	chr1:241799429..241802453-chr1:241804405..241808572,4	MCF-7	breast:
5	chr1:241801957..241807032-chr1:241808533..241817679,11	K562	blood:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12072899	1.00[MEX][hapmap]
rs2784165	0.86[ASW][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];0.91[AFR][1000 genomes]
rs595397	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs598292	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]
rs610693	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613797	0.86[ASW][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.94[AFR][1000 genomes]
rs615141	0.93[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[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]
rs9428514	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241803800-241806200	Flanking Active TSS	Hela-S3	cervix
2	chr1:241804000-241805600	Flanking Active TSS	HepG2	liver
3	chr1:241804000-241806200	Flanking Active TSS	A549	lung
4	chr1:241804200-241805400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:241804200-241805400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:241804200-241805400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:241804200-241805600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:241804200-241805600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:241804200-241805600	Enhancers	Stomach Mucosa	stomach
10	chr1:241804200-241805600	Enhancers	HUVEC	blood vessel
11	chr1:241804200-241805600	Enhancers	NHDF-Ad	bronchial
12	chr1:241804200-241805600	Enhancers	Osteobl	bone
13	chr1:241804200-241805800	Enhancers	Placenta	Placenta
14	chr1:241804200-241805800	Enhancers	NHEK	skin
15	chr1:241804200-241806800	Enhancers	Fetal Intestine Large	intestine
16	chr1:241804200-241808600	Weak transcription	Ovary	ovary
17	chr1:241804200-241809600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:241804400-241805800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:241804400-241809400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:241804400-241809600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:241804600-241805400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:241804600-241805600	Enhancers	NHLF	lung
23	chr1:241804800-241808600	Weak transcription	Gastric	stomach
24	chr1:241805000-241813600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:241805200-241805600	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr1:241805200-241806200	Enhancers	Liver	Liver

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