Variant report

Variant	rs1399941
Chromosome Location	chr6:93520886-93520887
allele	A/C
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	TCF12	chr6:93520665-93520888	GM12878	blood:	n/a	n/a
4	CTCF	chr6:93520490-93520971	MCF-7	breast:	n/a	chr6:93520886-93520899
5	RAD21	chr6:93520573-93520952	Hela-S3	cervix:	n/a	chr6:93520579-93520588
6	ATF2	chr6:93520527-93520984	GM12878	blood:	n/a	n/a
7	CTCF	chr6:93520626-93520904	MCF-7	breast:	n/a	chr6:93520886-93520899
8	CTCF	chr6:93520503-93521074	MCF-7	breast:	n/a	chr6:93520886-93520899
9	RAD21	chr6:93520512-93521047	ECC-1	luminal epithelium:	n/a	chr6:93520579-93520588
10	EBF1	chr6:93520725-93520962	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:93520707-93521101	H1-neurons	neurons:	n/a	n/a
12	CTCF	chr6:93520648-93520886	MCF-7	breast:	n/a	n/a
13	YY1	chr6:93520646-93520976	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr6:93520515-93520961	H1-hESC	embryonic stem cell:	n/a	chr6:93520579-93520588
15	PAX5	chr6:93520655-93520892	GM12878	blood:	n/a	n/a
16	RAD21	chr6:93520399-93521098	SK-N-SH	brain:	n/a	chr6:93520579-93520588
17	FOXA1	chr6:93520645-93521013	HepG2	liver:	n/a	n/a
18	STAT1	chr6:93520738-93520904	GM12878	blood:	n/a	n/a
19	CTCF	chr6:93520740-93520890	HCT-116	colon:	n/a	n/a
20	SMC3	chr6:93520387-93521091	SK-N-SH	brain:	n/a	chr6:93520750-93520760
21	RUNX3	chr6:93520601-93521007	GM12878	blood:	n/a	n/a
22	PAX5	chr6:93520526-93521087	GM12878	blood:	n/a	n/a
23	SPI1	chr6:93520634-93520903	GM12891	blood:	n/a	n/a
24	YY1	chr6:93520612-93520959	ECC-1	luminal epithelium:	n/a	n/a
25	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
26	YY1	chr6:93520715-93520915	HepG2	liver:	n/a	n/a
27	CTCF	chr6:93520591-93520893	Medullo	brain:	n/a	n/a
28	RAD21	chr6:93520630-93520896	HepG2	liver:	n/a	n/a
29	EP300	chr6:93520564-93520968	GM12878	blood:	n/a	n/a
30	CTCF	chr6:93520576-93520932	IMR90	lung:	n/a	chr6:93520886-93520899
31	YY1	chr6:93520652-93520893	K562	blood:	n/a	n/a
32	EP300	chr6:93520720-93520959	GM12878	blood:	n/a	n/a
33	NFATC1	chr6:93520614-93520974	GM12878	blood:	n/a	n/a
34	RAD21	chr6:93520578-93520922	GM12878	blood:	n/a	chr6:93520579-93520588
35	RAD21	chr6:93520578-93520932	HepG2	liver:	n/a	chr6:93520579-93520588
36	PAX5	chr6:93520629-93520895	GM12878	blood:	n/a	n/a
37	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
38	TCF7L2	chr6:93520602-93521010	MCF-7	breast:	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
39	CTCF	chr6:93520369-93521007	GM12878	blood:	n/a	chr6:93520886-93520899
40	FOXA2	chr6:93520640-93520926	HepG2	liver:	n/a	n/a
41	FOXA1	chr6:93520655-93520921	T-47D	breast:	n/a	n/a
42	CTCF	chr6:93520740-93520890	HCM	heart:	n/a	n/a
43	CTCF	chr6:93520518-93520959	HepG2	liver:	n/a	chr6:93520886-93520899
44	RAD21	chr6:93520565-93521032	H1-hESC	embryonic stem cell:	n/a	chr6:93520579-93520588
45	PAX5	chr6:93520653-93520993	GM12891	blood:	n/a	n/a
46	YY1	chr6:93520596-93520919	GM12878	blood:	n/a	n/a
47	RAD21	chr6:93520549-93520918	HepG2	liver:	n/a	chr6:93520579-93520588
48	MAZ	chr6:93520652-93520898	GM12878	blood:	n/a	n/a
49	RAD21	chr6:93520636-93520966	HCT-116	colon:	n/a	n/a
50	BCLAF1	chr6:93520535-93520895	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:93520687..93521206-chr6:93726686..93727450,3	MCF-7	breast:

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]
rs6902337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9294536	0.89[CHB][hapmap]
rs9294537	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]
rs9445025	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9452123	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9452134	0.88[ASN][1000 genomes]
rs9452135	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9452136	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9452137	0.90[ASN][1000 genomes]
rs9452138	0.90[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:4 , 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
4	chr6:93520800-93521200	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links