Variant report

Variant	rs4090553
Chromosome Location	chr19:41426757-41426758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:119)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:119 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr19:41426654-41427763	HepG2	liver:	n/a	n/a
2	EP300	chr19:41426628-41427755	T-47D	breast:	n/a	n/a
3	USF1	chr19:41426410-41427720	A549	lung:	n/a	n/a
4	SP1	chr19:41426158-41428226	A549	lung:	n/a	n/a
5	ZNF263	chr19:41426648-41427680	HEK293-T-REx	kidney:	n/a	n/a
6	TFAP2A	chr19:41426702-41427370	Hela-S3	cervix:	n/a	n/a
7	RAD21	chr19:41426638-41427819	A549	lung:	n/a	n/a
8	SP1	chr19:41426694-41427755	HCT-116	colon:	n/a	n/a
9	EP300	chr19:41426058-41428275	A549	lung:	n/a	chr19:41427952-41427966
10	KAP1	chr19:41426277-41427784	HEK293	kidney:	n/a	n/a
11	MAX	chr19:41426253-41428040	A549	lung:	n/a	n/a
12	NR3C1	chr19:41426550-41427867	A549	lung:	n/a	n/a
13	ESR1	chr19:41426454-41427805	T-47D	breast:	n/a	n/a
14	REST	chr19:41426567-41427854	A549	lung:	n/a	n/a
15	ESR1	chr19:41426427-41427907	T-47D	breast:	n/a	n/a
16	ETS1	chr19:41426627-41427814	A549	lung:	n/a	n/a
17	ZBTB33	chr19:41426638-41427811	A549	lung:	n/a	n/a
18	GATA3	chr19:41426485-41427991	A549	lung:	n/a	n/a
19	PBX3	chr19:41426691-41427640	A549	lung:	n/a	n/a
20	GATA3	chr19:41426639-41427843	MCF-7	breast:	n/a	n/a
21	BCL3	chr19:41426209-41428048	A549	lung:	n/a	n/a
22	JUND	chr19:41426696-41427515	Hela-S3	cervix:	n/a	chr19:41427099-41427110
23	SIN3AK20	chr19:41426324-41428111	A549	lung:	n/a	n/a
24	TCF12	chr19:41426535-41427890	A549	lung:	n/a	n/a
25	JUND	chr19:41426623-41427677	HCT-116	colon:	n/a	chr19:41427099-41427110
26	SIX5	chr19:41426003-41428376	A549	lung:	n/a	n/a
27	GATA3	chr19:41426514-41427742	T-47D	breast:	n/a	n/a
28	ESR1	chr19:41426343-41427897	T-47D	breast:	n/a	n/a
29	SMC3	chr19:41426728-41427491	Hela-S3	cervix:	n/a	n/a
30	ETS1	chr19:41426380-41428011	A549	lung:	n/a	n/a
31	KAP1	chr19:41426380-41427950	U2OS	brain:	n/a	n/a
32	JUND	chr19:41426702-41427690	HCT-116	colon:	n/a	chr19:41427099-41427110
33	USF1	chr19:41426701-41427613	A549	lung:	n/a	n/a
34	EP300	chr19:41426278-41428262	A549	lung:	n/a	chr19:41427952-41427966
35	NR3C1	chr19:41426691-41427799	A549	lung:	n/a	n/a
36	ATF3	chr19:41426280-41428001	A549	lung:	n/a	n/a
37	MAX	chr19:41426167-41428156	A549	lung:	n/a	n/a
38	NR3C1	chr19:41426570-41427861	A549	lung:	n/a	n/a
39	ESR1	chr19:41426376-41427929	T-47D	breast:	n/a	n/a
40	JUND	chr19:41426646-41427931	A549	lung:	n/a	chr19:41427099-41427110
41	EP300	chr19:41426670-41427539	Hela-S3	cervix:	n/a	n/a
42	SP1	chr19:41426223-41428603	A549	lung:	n/a	n/a
43	USF1	chr19:41426585-41427827	A549	lung:	n/a	n/a
44	NR2F2	chr19:41426718-41427807	MCF-7	breast:	n/a	n/a
45	FOSL1	chr19:41426702-41427688	HCT-116	colon:	n/a	n/a
46	TEAD4	chr19:41426665-41427814	A549	lung:	n/a	n/a
47	SP1	chr19:41426646-41427772	HCT-116	colon:	n/a	n/a
48	ELF1	chr19:41426630-41427806	A549	lung:	n/a	n/a
49	BCL3	chr19:41426105-41428005	A549	lung:	n/a	n/a
50	CEBPB	chr19:41426661-41427840	A549	lung:	n/a	chr19:41427674-41427685 chr19:41427674-41427685

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:41220910..41226186-chr19:41426409..41429163,5	MCF-7	breast:
2	chr19:41426562..41427465-chr19:41557958..41558773,3	MCF-7	breast:
3	chr19:41403631..41404535-chr19:41426743..41427640,3	MCF-7	breast:

No data

Variant related genes	Relation type
CYP2B7P	TF binding region
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10419450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420231	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12459565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844445	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3852872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3933911	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4001945	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59046772	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508960	0.94[ASN][1000 genomes]
rs7247910	0.94[ASN][1000 genomes]
rs7248187	0.93[ASN][1000 genomes]
rs7249124	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv3337314	chr19:41388910-41534583	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv437830	chr19:41408746-41515702	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv437831	chr19:41416072-41524087	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41426200-41427600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr19:41426200-41429800	Enhancers	Stomach Mucosa	stomach
3	chr19:41426400-41427600	Weak transcription	Colonic Mucosa	Colon
4	chr19:41426400-41427800	Enhancers	HepG2	liver
5	chr19:41426400-41428000	Enhancers	Hela-S3	cervix
6	chr19:41426400-41429600	Enhancers	Ovary	ovary
7	chr19:41426400-41430200	Enhancers	Fetal Intestine Large	intestine
8	chr19:41426400-41430200	Enhancers	Fetal Intestine Small	intestine
9	chr19:41426600-41426800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr19:41426600-41426800	Flanking Active TSS	A549	lung
11	chr19:41426600-41427000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:41426600-41427400	Enhancers	HUVEC	blood vessel
13	chr19:41426600-41428200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:41426600-41429000	Enhancers	K562	blood
15	chr19:41426600-41429600	Enhancers	Liver	Liver

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