Variant report

Variant	rs6690411
Chromosome Location	chr1:241685275-241685276
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	EP300	chr1:241685048-241685345	HepG2	liver:	n/a	n/a
2	FOXA1	chr1:241684976-241685356	HepG2	liver:	n/a	n/a
3	FOXA2	chr1:241684380-241685929	HepG2	liver:	n/a	n/a
4	NFIC	chr1:241684917-241685443	HepG2	liver:	n/a	n/a
5	MYBL2	chr1:241684928-241685430	HepG2	liver:	n/a	n/a
6	FOXA1	chr1:241684965-241685904	HepG2	liver:	n/a	n/a
7	HNF4A	chr1:241685073-241685368	HepG2	liver:	n/a	chr1:241685133-241685147 chr1:241685132-241685147 chr1:241685138-241685146
8	FOXA1	chr1:241685012-241685441	HepG2	liver:	n/a	n/a
9	TCF7L2	chr1:241685044-241685481	HepG2	liver:	n/a	n/a
10	GATA3	chr1:241685164-241685517	SH-SY5Y	brain:	n/a	n/a
11	HNF4A	chr1:241685065-241685279	HepG2	liver:	n/a	chr1:241685133-241685147 chr1:241685132-241685147 chr1:241685138-241685146
12	FOXA2	chr1:241685063-241685322	HepG2	liver:	n/a	n/a
13	FOXA1	chr1:241684921-241685924	HepG2	liver:	n/a	n/a
14	ARID3A	chr1:241685036-241685352	HepG2	liver:	n/a	n/a
15	SP1	chr1:241685019-241685406	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:241681125..241684072-chr1:241685116..241687074,3	MCF-7	breast:
2	chr1:241683433..241685881-chr1:241689141..241691385,3	MCF-7	breast:
3	chr1:241684656..241686191-chr1:242009808..242012105,2	K562	blood:
4	chr1:241677220..241680834-chr1:241684726..241688550,4	K562	blood:

Variant related genes	Relation type
FH	TF binding region
ENSG00000174371	Chromatin interaction
ENSG00000091483	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10802969	0.87[EUR][1000 genomes]
rs10926505	0.87[EUR][1000 genomes]
rs10926508	0.87[EUR][1000 genomes]
rs10926510	0.87[EUR][1000 genomes]
rs12064150	0.87[EUR][1000 genomes]
rs12076255	0.87[EUR][1000 genomes]
rs12079341	0.87[EUR][1000 genomes]
rs16841808	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275162	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765802	0.87[EUR][1000 genomes]
rs3765803	0.88[ASN][1000 genomes]
rs3765804	0.87[EUR][1000 genomes]
rs3819976	0.87[EUR][1000 genomes]
rs4659609	0.87[EUR][1000 genomes]
rs4660101	0.87[EUR][1000 genomes]
rs56957678	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58766151	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59625977	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60043538	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60673334	0.84[ASN][1000 genomes]
rs61543265	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61737760	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6429277	0.87[EUR][1000 genomes]
rs6429278	0.87[EUR][1000 genomes]
rs66482665	0.87[EUR][1000 genomes]
rs66497254	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66626588	0.88[ASN][1000 genomes]
rs66669018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66710178	0.87[EUR][1000 genomes]
rs6678986	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66799800	0.96[ASN][1000 genomes]
rs6681649	0.87[EUR][1000 genomes]
rs6684064	0.87[EUR][1000 genomes]
rs6687609	0.87[EUR][1000 genomes]
rs6698519	0.87[EUR][1000 genomes]
rs67219057	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67267325	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67439618	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67528386	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67794990	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67802946	0.82[EUR][1000 genomes]
rs68119865	0.84[ASN][1000 genomes]
rs68147305	0.87[EUR][1000 genomes]
rs72766004	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73135296	0.88[ASN][1000 genomes]
rs73137530	0.87[EUR][1000 genomes]
rs7539730	0.87[EUR][1000 genomes]

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	nsv949442	chr1:241432051-241730054	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv873371	chr1:241667244-241747838	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241684200-241686200	Enhancers	Liver	Liver
2	chr1:241684200-241688400	Weak transcription	K562	blood
3	chr1:241685000-241686000	Enhancers	HepG2	liver

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