Variant report

Variant	rs682088
Chromosome Location	chr6:54172465-54172466
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	FOXA1	chr6:54172126-54172764	HepG2	liver:	n/a	n/a
2	FOXA2	chr6:54172123-54172687	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:54172095-54172758	HepG2	liver:	n/a	n/a
4	HNF4A	chr6:54172173-54172546	HepG2	liver:	n/a	chr6:54172365-54172380
5	TBP	chr6:54172318-54172601	HepG2	liver:	n/a	n/a
6	EP300	chr6:54172105-54172693	HepG2	liver:	n/a	n/a
7	MAFK	chr6:54172283-54172594	HepG2	liver:	n/a	chr6:54172432-54172441
8	ARID3A	chr6:54172209-54172486	HepG2	liver:	n/a	n/a
9	MAFK	chr6:54172322-54172568	HepG2	liver:	n/a	chr6:54172432-54172441
10	FOSL2	chr6:54172258-54172622	HepG2	liver:	n/a	n/a
11	MYBL2	chr6:54172124-54172728	HepG2	liver:	n/a	n/a
12	REST	chr6:54172242-54172504	HepG2	liver:	n/a	n/a
13	SP1	chr6:54172147-54172722	HepG2	liver:	n/a	n/a
14	FOXA1	chr6:54172073-54172716	HepG2	liver:	n/a	n/a
15	NR3C1	chr6:54172348-54172781	A549	lung:	n/a	n/a
16	MBD4	chr6:54172119-54172604	HepG2	liver:	n/a	n/a
17	RPC155	chr6:54172179-54172578	Hela-S3	cervix:	n/a	n/a
18	JUND	chr6:54172308-54172517	HepG2	liver:	n/a	chr6:54172432-54172443
19	MAFK	chr6:54172455-54172525	H1-hESC	embryonic stem cell:	n/a	n/a
20	RELA	chr6:54172203-54173624	GM19099	blood:	n/a	n/a
21	MAFF	chr6:54172266-54172612	HepG2	liver:	n/a	chr6:54172425-54172443
22	NFIC	chr6:54172188-54172713	HepG2	liver:	n/a	n/a
23	HDAC2	chr6:54172222-54172583	HepG2	liver:	n/a	chr6:54172227-54172235 chr6:54172491-54172500
24	FOXA1	chr6:54172314-54172679	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
TINAG	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1058768	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1316576	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1353708	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs1508638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605675	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1605676	0.85[CEU][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1848439	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1934791	1.00[CEU][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1995768	0.88[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs2202802	0.94[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2221666	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2297981	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3777652	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs3798278	0.81[AMR][1000 genomes]
rs6458994	0.94[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7740868	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7740970	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7754752	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7760842	0.87[CEU][hapmap];0.81[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7766669	0.86[AMR][1000 genomes]
rs9367561	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9367562	0.88[CEU][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs682088	ZNF451	cis	cerebellum	SCAN
rs682088	TINAG	Cis_1M	lymphoblastoid	RTeQTL
rs682088	GSTA1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54168800-54176400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:54171600-54172800	Enhancers	Fetal Intestine Large	intestine
3	chr6:54171800-54172600	Enhancers	Fetal Intestine Small	intestine
4	chr6:54171800-54173800	Enhancers	HepG2	liver
5	chr6:54171800-54176600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:54172200-54176200	Active TSS	Fetal Kidney	kidney
7	chr6:54172400-54172600	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr6:54172400-54172600	Active TSS	A549	lung
9	chr6:54172400-54176600	Active TSS	Duodenum Mucosa	Duodenum

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