Variant report

Variant	rs9294537
Chromosome Location	chr6:93520592-93520593
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	TCF7L2	chr6:93520579-93520998	PANC-1	pancreas:	n/a	chr6:93520778-93520785 chr6:93520824-93520838 chr6:93520824-93520840 chr6:93520701-93520711 chr6:93520827-93520836 chr6:93520829-93520836 chr6:93520828-93520837 chr6:93520907-93520921 chr6:93520824-93520840 chr6:93520778-93520788
2	SMC3	chr6:93520572-93520933	HepG2	liver:	n/a	chr6:93520750-93520760
3	CTCF	chr6:93520490-93520971	MCF-7	breast:	n/a	chr6:93520886-93520899
4	RAD21	chr6:93520573-93520952	Hela-S3	cervix:	n/a	chr6:93520579-93520588
5	ATF2	chr6:93520527-93520984	GM12878	blood:	n/a	n/a
6	CTCF	chr6:93520500-93520650	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr6:93520503-93521074	MCF-7	breast:	n/a	chr6:93520886-93520899
8	RAD21	chr6:93520512-93521047	ECC-1	luminal epithelium:	n/a	chr6:93520579-93520588
9	RAD21	chr6:93520515-93520961	H1-hESC	embryonic stem cell:	n/a	chr6:93520579-93520588
10	RAD21	chr6:93520399-93521098	SK-N-SH	brain:	n/a	chr6:93520579-93520588
11	SMC3	chr6:93520387-93521091	SK-N-SH	brain:	n/a	chr6:93520750-93520760
12	PAX5	chr6:93520526-93521087	GM12878	blood:	n/a	n/a
13	TCF7L2	chr6:93520535-93521155	HCT-116	colon:	n/a	chr6:93520778-93520785 chr6:93520824-93520838 chr6:93520824-93520840 chr6:93520701-93520711 chr6:93520827-93520836 chr6:93520829-93520836 chr6:93520828-93520837 chr6:93520907-93520921 chr6:93520824-93520840 chr6:93520778-93520788
14	CTCF	chr6:93520591-93520893	Medullo	brain:	n/a	n/a
15	EP300	chr6:93520564-93520968	GM12878	blood:	n/a	n/a
16	CTCF	chr6:93520576-93520932	IMR90	lung:	n/a	chr6:93520886-93520899
17	RAD21	chr6:93520588-93520838	SK-N-SH_RA	brain:	n/a	n/a
18	RAD21	chr6:93520578-93520922	GM12878	blood:	n/a	chr6:93520579-93520588
19	CTCF	chr6:93520520-93520670	HFF-Myc	foreskin:	n/a	n/a
20	RAD21	chr6:93520578-93520932	HepG2	liver:	n/a	chr6:93520579-93520588
21	TCF7L2	chr6:93520550-93521014	Hela-S3	cervix:	n/a	chr6:93520778-93520785 chr6:93520824-93520838 chr6:93520824-93520840 chr6:93520701-93520711 chr6:93520827-93520836 chr6:93520829-93520836 chr6:93520828-93520837 chr6:93520907-93520921 chr6:93520824-93520840 chr6:93520778-93520788
22	CTCF	chr6:93520369-93521007	GM12878	blood:	n/a	chr6:93520886-93520899
23	CTCF	chr6:93520518-93520959	HepG2	liver:	n/a	chr6:93520886-93520899
24	RAD21	chr6:93520565-93521032	H1-hESC	embryonic stem cell:	n/a	chr6:93520579-93520588
25	CTCF	chr6:93520580-93520730	GM12873	blood:	n/a	n/a
26	RAD21	chr6:93520549-93520918	HepG2	liver:	n/a	chr6:93520579-93520588
27	BCLAF1	chr6:93520535-93520895	GM12878	blood:	n/a	n/a
28	TCF7L2	chr6:93520442-93521205	HEK293	kidney:	n/a	chr6:93520778-93520785 chr6:93520824-93520838 chr6:93520824-93520840 chr6:93520701-93520711 chr6:93520827-93520836 chr6:93520829-93520836 chr6:93520828-93520837 chr6:93520907-93520921 chr6:93520824-93520840 chr6:93520778-93520788
29	RAD21	chr6:93520568-93520955	GM12878	blood:	n/a	chr6:93520579-93520588
30	PML	chr6:93520516-93521039	GM12878	blood:	n/a	n/a
31	RUNX3	chr6:93520592-93520916	GM12878	blood:	n/a	n/a
32	SMC3	chr6:93520576-93520963	Hela-S3	cervix:	n/a	chr6:93520750-93520760
33	CTCF	chr6:93520455-93521031	A549	lung:	n/a	chr6:93520886-93520899
34	CTCF	chr6:93520553-93520897	H1-hESC	embryonic stem cell:	n/a	n/a
35	RCOR1	chr6:93520581-93520921	GM12878	blood:	n/a	n/a
36	SMC3	chr6:93520567-93520994	GM12878	blood:	n/a	chr6:93520750-93520760
37	RAD21	chr6:93520461-93521022	H1-hESC	embryonic stem cell:	n/a	chr6:93520579-93520588
38	RAD21	chr6:93520536-93520989	ECC-1	luminal epithelium:	n/a	chr6:93520579-93520588
39	CTCF	chr6:93520390-93521149	SK-N-SH	brain:	n/a	chr6:93520886-93520899
40	ZNF143	chr6:93520576-93520953	GM12878	blood:	n/a	n/a
41	RAD21	chr6:93520385-93521156	MCF-7	breast:	n/a	chr6:93520579-93520588
42	RAD21	chr6:93520570-93520867	GM12878	blood:	n/a	chr6:93520579-93520588
43	CTCF	chr6:93520580-93520730	HFF	foreskin:	n/a	n/a
44	RAD21	chr6:93520485-93521055	MCF-7	breast:	n/a	chr6:93520579-93520588
45	CTCF	chr6:93520579-93520924	K562	blood:	n/a	chr6:93520886-93520899
46	RAD21	chr6:93520548-93520970	SK-N-SH_RA	brain:	n/a	chr6:93520579-93520588
47	FOXA1	chr6:93520546-93520941	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000238412	TF binding region

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11962323	0.89[CHB][hapmap]
rs11964555	0.88[CHB][hapmap]
rs11970040	0.88[CHB][hapmap]
rs1399941	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1515788	0.81[AFR][1000 genomes]
rs6902337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922609	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922656	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9445025	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9452123	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9452134	0.86[ASN][1000 genomes]
rs9452135	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9452136	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9452137	0.88[ASN][1000 genomes]
rs9452138	0.88[ASN][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	nsv886355	chr6:93166766-93530757	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1018402	chr6:93173579-93855804	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1031496	chr6:93365937-93715883	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv428150	chr6:93409468-93587278	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017311	chr6:93432753-93559750	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv463960	chr6:93512325-93570432	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv604149	chr6:93512325-93570432	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 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	chr6:93520400-93521000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:93520400-93521200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:93520400-93521800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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