Variant report

Variant	rs12563398
Chromosome Location	chr1:168721877-168721878
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	SP1	chr1:168721125-168721957	A549	lung:	n/a	chr1:168721792-168721804 chr1:168721793-168721807 chr1:168721792-168721804 chr1:168721794-168721803
2	CEBPB	chr1:168721185-168721901	A549	lung:	n/a	chr1:168721347-168721358 chr1:168721347-168721358
3	MAX	chr1:168721353-168722006	Hela-S3	cervix:	n/a	chr1:168721793-168721803
4	SMC3	chr1:168721253-168721918	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr1:168721208-168721879	MCF-7	breast:	n/a	chr1:168721347-168721358 chr1:168721347-168721358
6	KAP1	chr1:168720220-168721969	U2OS	brain:	n/a	chr1:168721501-168721510
7	SIN3AK20	chr1:168721140-168721902	MCF-7	breast:	n/a	n/a
8	CEBPB	chr1:168721165-168721881	MCF-7	breast:	n/a	chr1:168721347-168721358 chr1:168721347-168721358
9	SP1	chr1:168721099-168722131	A549	lung:	n/a	chr1:168721792-168721804 chr1:168721793-168721807 chr1:168721792-168721804 chr1:168721794-168721803
10	FOXA2	chr1:168721239-168721995	A549	lung:	n/a	n/a
11	REST	chr1:168721238-168721906	A549	lung:	n/a	chr1:168721674-168721681
12	EP300	chr1:168721164-168721918	A549	lung:	n/a	chr1:168721628-168721637 chr1:168721503-168721512
13	GATA3	chr1:168721233-168721898	MCF-7	breast:	n/a	chr1:168721635-168721642 chr1:168721631-168721647 chr1:168721628-168721649 chr1:168721635-168721644 chr1:168721634-168721644
14	FOSL2	chr1:168721072-168722013	A549	lung:	n/a	chr1:168721502-168721511 chr1:168721089-168721101 chr1:168721502-168721512 chr1:168721503-168721512 chr1:168721503-168721510
15	GATA3	chr1:168721028-168721921	MCF-7	breast:	n/a	chr1:168721635-168721642 chr1:168721631-168721647 chr1:168721628-168721649 chr1:168721635-168721644 chr1:168721634-168721644
16	MAX	chr1:168721227-168722022	A549	lung:	n/a	chr1:168721793-168721803
17	EP300	chr1:168721247-168721901	Hela-S3	cervix:	n/a	chr1:168721628-168721637 chr1:168721503-168721512
18	GATA3	chr1:168721171-168722088	A549	lung:	n/a	chr1:168721635-168721642 chr1:168721631-168721647 chr1:168721628-168721649 chr1:168721635-168721644 chr1:168721634-168721644
19	EP300	chr1:168721039-168722061	A549	lung:	n/a	chr1:168721628-168721637 chr1:168721503-168721512
20	STAT3	chr1:168721288-168721909	Hela-S3	cervix:	n/a	chr1:168721502-168721511
21	TCF12	chr1:168721077-168722056	A549	lung:	n/a	n/a
22	CEBPB	chr1:168721135-168721935	A549	lung:	n/a	chr1:168721347-168721358 chr1:168721347-168721358
23	MAX	chr1:168721333-168721954	Hela-S3	cervix:	n/a	chr1:168721793-168721803
24	KAP1	chr1:168720384-168722037	HEK293	kidney:	n/a	chr1:168721501-168721510
25	GTF2F1	chr1:168721441-168721885	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168721671..168723479-chr1:168723958..168727658,3	MCF-7	breast:
2	chr1:168717969..168723195-chr1:169075012..169079192,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221578	TF binding region
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1018453	0.89[ASN][1000 genomes]
rs10489362	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052591	0.89[ASN][1000 genomes]
rs10800378	0.84[ASN][1000 genomes]
rs12567476	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724380	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12728858	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731369	0.89[ASN][1000 genomes]
rs12735097	0.94[ASN][1000 genomes]
rs12737253	0.81[AMR][1000 genomes]
rs12739280	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12742262	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12748557	0.94[ASN][1000 genomes]
rs12755391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555206	0.90[ASN][1000 genomes]
rs1556790	0.91[ASN][1000 genomes]
rs1556791	0.91[ASN][1000 genomes]
rs1556792	0.91[ASN][1000 genomes]
rs1556793	0.91[ASN][1000 genomes]
rs17569416	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1765516	0.94[ASN][1000 genomes]
rs1765517	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989300	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206288	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744658	0.89[ASN][1000 genomes]
rs2744659	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744665	0.84[ASN][1000 genomes]
rs2786758	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2786759	0.84[ASN][1000 genomes]
rs2786760	0.97[ASN][1000 genomes]
rs2786762	0.84[ASN][1000 genomes]
rs35723976	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs472668	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484025	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485109	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485855	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489585	1.00[ASN][1000 genomes]
rs525275	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534139	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538714	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542198	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552859	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs555676	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609629	0.96[ASN][1000 genomes]
rs610403	0.96[ASN][1000 genomes]
rs623949	0.96[ASN][1000 genomes]
rs625712	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627872	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427149	0.99[ASN][1000 genomes]
rs6427150	0.84[ASN][1000 genomes]
rs655128	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656919	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666079	0.94[ASN][1000 genomes]
rs6675239	0.84[ASN][1000 genomes]
rs6678818	0.94[ASN][1000 genomes]
rs6687926	0.80[ASN][1000 genomes]
rs6688024	0.96[AFR][1000 genomes]
rs6688207	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6690929	0.84[ASN][1000 genomes]
rs6693709	0.81[ASN][1000 genomes]
rs6697889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701299	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672950	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686610	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731949	0.89[ASN][1000 genomes]
rs734123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760913	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763433	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926431	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168711200-168724200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:168720000-168722000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:168720400-168722000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:168720600-168722200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:168720600-168722600	Enhancers	Fetal Lung	lung
6	chr1:168720800-168722000	Flanking Active TSS	A549	lung
7	chr1:168720800-168722000	Bivalent Enhancer	HepG2	liver
8	chr1:168720800-168724000	Weak transcription	Fetal Heart	heart
9	chr1:168721000-168723600	Weak transcription	Fetal Kidney	kidney
10	chr1:168721000-168723800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:168721200-168725400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:168721400-168722000	Enhancers	Stomach Mucosa	stomach
13	chr1:168721400-168725200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:168721600-168722000	Enhancers	Colonic Mucosa	Colon
15	chr1:168721600-168722000	Enhancers	Right Atrium	heart
16	chr1:168721600-168722000	Flanking Active TSS	Hela-S3	cervix
17	chr1:168721600-168722200	Enhancers	Fetal Intestine Large	intestine
18	chr1:168721600-168722200	Enhancers	Fetal Intestine Small	intestine
19	chr1:168721800-168722000	Enhancers	Pancreas	Pancrea

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