Variant report

Variant	rs2682844
Chromosome Location	chr2:56976347-56976348
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	chr2:56976326-56976648	GM12878	blood:	n/a	n/a
2	RAD21	chr2:56976202-56976807	A549	lung:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
3	CTCF	chr2:56976299-56976715	IMR90	lung:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
4	CTCF	chr2:56976337-56976654	K562	blood:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
5	RAD21	chr2:56976112-56977060	SK-N-SH	brain:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
6	SMC3	chr2:56976335-56976670	HepG2	liver:	n/a	chr2:56976488-56976502
7	RAD21	chr2:56976257-56976663	H1-hESC	embryonic stem cell:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
8	CTCF	chr2:56975808-56976853	A549	lung:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
9	CTCF	chr2:56976336-56976707	MCF-7	breast:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
10	CTCF	chr2:56976226-56976820	HCT-116	colon:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
11	RAD21	chr2:56976324-56976738	A549	lung:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
12	FOS	chr2:56976339-56976616	MCF10A-Er-Src	breast:	n/a	chr2:56976451-56976462 chr2:56976451-56976458
13	RAD21	chr2:56976327-56976718	HCT-116	colon:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
14	CTCF	chr2:56976324-56976663	SK-N-SH_RA	brain:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
15	CTCF	chr2:56976294-56976704	GM12878	blood:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
16	RAD21	chr2:56976315-56976724	IMR90	lung:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
17	STAT3	chr2:56976314-56976594	MCF10A-Er-Src	breast:	n/a	chr2:56976438-56976449
18	SMC3	chr2:56976320-56976714	GM12878	blood:	n/a	chr2:56976488-56976502
19	STAT3	chr2:56976287-56976623	MCF10A-Er-Src	breast:	n/a	chr2:56976438-56976449
20	RAD21	chr2:56976295-56976678	Hela-S3	cervix:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
21	FOS	chr2:56976329-56976627	HUVEC	blood vessel:	n/a	chr2:56976451-56976462 chr2:56976451-56976458
22	FOS	chr2:56976332-56976619	MCF10A-Er-Src	breast:	n/a	chr2:56976451-56976462 chr2:56976451-56976458
23	SMC3	chr2:56976305-56976673	Hela-S3	cervix:	n/a	chr2:56976488-56976502
24	RAD21	chr2:56976334-56976700	HepG2	liver:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
25	RAD21	chr2:56976329-56976755	MCF-7	breast:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
26	RAD21	chr2:56976275-56976632	HepG2	liver:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
27	RAD21	chr2:56976258-56976729	ECC-1	luminal epithelium:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
28	CTCF	chr2:56976325-56976722	MCF-7	breast:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
29	CTCF	chr2:56976340-56976490	GM12868	blood:	n/a	n/a
30	SMC3	chr2:56975926-56976987	SK-N-SH	brain:	n/a	chr2:56976488-56976502
31	CTCF	chr2:56976340-56976490	HAc	cerebellar:	n/a	n/a
32	CTCF	chr2:56976268-56976703	A549	lung:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
33	RAD21	chr2:56976301-56976721	H1-hESC	embryonic stem cell:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
34	RAD21	chr2:56976260-56976802	HCT-116	colon:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
35	RAD21	chr2:56976285-56976729	SK-N-SH_RA	brain:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
36	CTCF	chr2:56976319-56977050	SK-N-SH	brain:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
37	CTCF	chr2:56976260-56976410	HFF	foreskin:	n/a	n/a
38	CTCF	chr2:56976340-56976490	GM12873	blood:	n/a	n/a
39	RAD21	chr2:56976265-56976684	SK-N-SH_RA	brain:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
40	RAD21	chr2:56976292-56976667	GM12878	blood:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
41	STAT3	chr2:56976336-56976542	MCF10A-Er-Src	breast:	n/a	chr2:56976438-56976449
42	RAD21	chr2:56976184-56976812	MCF-7	breast:	n/a	chr2:56976494-56976501 chr2:56976484-56976503
43	CTCF	chr2:56976325-56976681	HepG2	liver:	n/a	chr2:56976487-56976503 chr2:56976486-56976504 chr2:56976491-56976499 chr2:56976488-56976501 chr2:56976481-56976502
44	CTCF	chr2:56976340-56976490	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:56418873..56419603-chr2:56975911..56976760,2	MCF-7	breast:
2	chr2:56410661..56411329-chr2:56976031..56976883,5	MCF-7	breast:
3	chr2:56410374..56411316-chr2:56976212..56976966,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231570	TF binding region
ENSG00000055813	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10175703	0.86[AFR][1000 genomes]
rs10175921	0.82[AFR][1000 genomes]
rs10193478	0.81[AFR][1000 genomes]
rs1019426	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1019427	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779941	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885280	0.86[AFR][1000 genomes]
rs11885371	0.86[AFR][1000 genomes]
rs11894249	0.86[AFR][1000 genomes]
rs11897725	0.81[AFR][1000 genomes]
rs13387012	0.82[AFR][1000 genomes]
rs13415063	0.86[AFR][1000 genomes]
rs1468998	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042124	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2193813	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193815	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193816	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193817	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544314	0.91[EUR][1000 genomes]
rs2682838	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682839	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682840	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682841	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682842	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682843	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682846	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682847	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682848	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671295	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672159	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6545594	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6729559	0.86[AFR][1000 genomes]
rs6730067	0.86[AFR][1000 genomes]
rs6742211	0.81[AFR][1000 genomes]
rs6758203	0.86[AFR][1000 genomes]
rs764798	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs978566	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	nsv1008859	chr2:56767452-57126026	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv535726	chr2:56767452-57126026	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv582058	chr2:56892585-57016392	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv582059	chr2:56892585-57175087	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535727	chr2:56895497-57059359	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1007347	chr2:56904928-57100439	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv582060	chr2:56941668-57137622	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56969000-56978600	Weak transcription	Aorta	Aorta

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