Variant report

Variant	rs11928816
Chromosome Location	chr3:89098328-89098329
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	ZNF143	chr3:89098264-89098623	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr3:89098290-89098620	GM12878	blood:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
3	CTCF	chr3:89098280-89098520	HepG2	liver:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
4	CTCF	chr3:89098227-89098613	H1-hESC	embryonic stem cell:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
5	CTCF	chr3:89098200-89098350	A549	lung:	n/a	n/a
6	RAD21	chr3:89098279-89098611	IMR90	lung:	n/a	chr3:89098584-89098594
7	CTCF	chr3:89098320-89098470	GM12864	blood:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
8	RAD21	chr3:89098230-89098720	ECC-1	luminal epithelium:	n/a	chr3:89098258-89098267 chr3:89098584-89098594
9	CTCF	chr3:89098320-89098470	HA-sp	spinal cord:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
10	CTCF	chr3:89098320-89098470	GM12868	blood:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
11	RAD21	chr3:89098306-89098694	ECC-1	luminal epithelium:	n/a	chr3:89098584-89098594
12	CTCF	chr3:89098320-89098470	HEEpiC	esophagus:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
13	CTCF	chr3:89098300-89098450	GM06990	blood:	n/a	n/a
14	CTCF	chr3:89098300-89098450	AoAF	blood vessel:	n/a	n/a
15	CTCF	chr3:89098180-89098676	MCF-7	breast:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
16	RAD21	chr3:89098173-89098707	MCF-7	breast:	n/a	chr3:89098258-89098267 chr3:89098584-89098594
17	RAD21	chr3:89098318-89098581	HepG2	liver:	n/a	n/a
18	CTCF	chr3:89098298-89098585	H1-hESC	embryonic stem cell:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
19	RAD21	chr3:89098311-89098632	HepG2	liver:	n/a	chr3:89098584-89098594
20	CTCF	chr3:89098320-89098470	NHDF-neo	bronchial:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
21	CTCF	chr3:89098300-89098450	HVMF	connective:	n/a	n/a
22	CTCF	chr3:89098286-89098600	IMR90	lung:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
23	RAD21	chr3:89098269-89098509	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr3:89098320-89098470	HRE	kidney:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
25	RAD21	chr3:89098102-89098740	H1-hESC	embryonic stem cell:	n/a	chr3:89098258-89098267 chr3:89098584-89098594
26	CTCF	chr3:89098320-89098470	HPAF	blood vessel:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
27	RAD21	chr3:89098272-89098568	HepG2	liver:	n/a	n/a
28	CTCF	chr3:89098280-89098430	HCM	heart:	n/a	n/a
29	RAD21	chr3:89098229-89098641	H1-hESC	embryonic stem cell:	n/a	chr3:89098258-89098267 chr3:89098584-89098594
30	RAD21	chr3:89098279-89098637	H1-hESC	embryonic stem cell:	n/a	chr3:89098584-89098594
31	CTCF	chr3:89098326-89098538	HepG2	liver:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
32	RAD21	chr3:89098258-89098594	MCF-7	breast:	n/a	chr3:89098258-89098267 chr3:89098584-89098594
33	CTCF	chr3:89098300-89098450	GM12872	blood:	n/a	n/a
34	CTCF	chr3:89098320-89098470	GM12874	blood:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
35	CTCF	chr3:89098320-89098470	BJ	skin:	n/a	chr3:89098447-89098456 chr3:89098441-89098459
36	GTF2F1	chr3:89098311-89098512	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
GAPDHP50	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11927219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6801565	1.00[EUR][1000 genomes]
rs73845978	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834759	chr3:88901229-89105366	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv877158	chr3:89018866-89103302	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877160	chr3:89051475-89135125	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89098000-89098400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:89098200-89098400	Enhancers	HUES48 Cell Line	embryonic stem cell

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