Variant report

Variant	rs12465052
Chromosome Location	chr2:208926883-208926884
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:82)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:82 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:208926763-208927267	ECC-1	luminal epithelium:	n/a	n/a
2	RAD21	chr2:208926883-208927080	GM12878	blood:	n/a	n/a
3	RAD21	chr2:208926845-208927154	SK-N-SH_RA	brain:	n/a	n/a
4	JUND	chr2:208926862-208927198	H1-hESC	embryonic stem cell:	n/a	chr2:208927048-208927059
5	RAD21	chr2:208926753-208927217	MCF-7	breast:	n/a	n/a
6	CTCF	chr2:208926880-208927030	AG10803	skin:	n/a	n/a
7	ATF1	chr2:208926861-208927192	K562	blood:	n/a	n/a
8	CTCF	chr2:208926880-208927030	SK-N-SH_RA	brain:	n/a	n/a
9	PML	chr2:208926827-208927098	K562	blood:	n/a	n/a
10	RAD21	chr2:208926840-208927171	SK-N-SH_RA	brain:	n/a	n/a
11	RCOR1	chr2:208926832-208927156	K562	blood:	n/a	n/a
12	RAD21	chr2:208926879-208927047	K562	blood:	n/a	n/a
13	CTCF	chr2:208926880-208927030	SAEC	small airway:	n/a	n/a
14	TAL1	chr2:208926700-208927221	K562	blood:	n/a	n/a
15	TEAD4	chr2:208926776-208927224	K562	blood:	n/a	n/a
16	CTCF	chr2:208926729-208927177	HCT-116	colon:	n/a	n/a
17	GATA2	chr2:208926783-208927195	K562	blood:	n/a	n/a
18	CTCF	chr2:208926832-208927187	A549	lung:	n/a	n/a
19	CEBPD	chr2:208926804-208927269	K562	blood:	n/a	n/a
20	CTCF	chr2:208926811-208927189	HepG2	liver:	n/a	n/a
21	CEBPD	chr2:208926854-208927199	K562	blood:	n/a	n/a
22	CTCF	chr2:208926880-208927030	NHEK	skin:	n/a	n/a
23	CTCF	chr2:208926860-208927010	RPTEC	kidney:	n/a	n/a
24	CTCF	chr2:208926880-208927030	HepG2	liver:	n/a	n/a
25	CTCF	chr2:208926880-208927030	GM12878	blood:	n/a	n/a
26	CTCF	chr2:208926840-208926990	GM12873	blood:	n/a	n/a
27	SMC3	chr2:208926840-208927164	GM12878	blood:	n/a	n/a
28	RAD21	chr2:208926805-208927176	HepG2	liver:	n/a	n/a
29	RAD21	chr2:208926790-208927190	H1-hESC	embryonic stem cell:	n/a	n/a
30	EP300	chr2:208926826-208927200	K562	blood:	n/a	n/a
31	CTCF	chr2:208926883-208927086	A549	lung:	n/a	n/a
32	CTCF	chr2:208926880-208927030	WERI-Rb-1	eye:	n/a	n/a
33	FOSL2	chr2:208926808-208927221	A549	lung:	n/a	n/a
34	UBTF	chr2:208926833-208926992	K562	blood:	n/a	n/a
35	RAD21	chr2:208926816-208927184	IMR90	lung:	n/a	n/a
36	CTCF	chr2:208926831-208927205	K562	blood:	n/a	n/a
37	ATF3	chr2:208926822-208927209	K562	blood:	n/a	n/a
38	JUND	chr2:208926833-208927254	K562	blood:	n/a	chr2:208927048-208927059
39	FOS	chr2:208926871-208927153	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr2:208926747-208927217	A549	lung:	n/a	n/a
41	CTCF	chr2:208926864-208927084	HepG2	liver:	n/a	n/a
42	CTCF	chr2:208926873-208927124	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr2:208926691-208927336	HCT-116	colon:	n/a	n/a
44	SMC3	chr2:208926835-208927163	HepG2	liver:	n/a	n/a
45	RAD21	chr2:208926615-208927225	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr2:208926860-208927010	HFF-Myc	foreskin:	n/a	n/a
47	CTCF	chr2:208926880-208927030	GM12866	blood:	n/a	n/a
48	MAFK	chr2:208926868-208927123	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr2:208926867-208927244	ECC-1	luminal epithelium:	n/a	n/a
50	RAD21	chr2:208926821-208927155	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:208393455..208396354-chr2:208925710..208928306,2	K562	blood:
2	chr2:208926371..208927250-chr2:208936763..208937685,3	MCF-7	breast:
3	chr2:208610533..208611358-chr2:208926502..208927536,4	MCF-7	breast:
4	chr2:208926513..208930859-chr2:208931530..208934190,4	K562	blood:
5	chr2:208489759..208491901-chr2:208925964..208928924,2	K562	blood:
6	chr2:208925382..208927634-chr2:208938153..208941077,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224839	TF binding region
ENSG00000144401	Chromatin interaction
ENSG00000238582	Chromatin interaction
ENSG00000223725	Chromatin interaction
ENSG00000118260	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10192860	0.94[EUR][1000 genomes]
rs10497895	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10932224	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12464255	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12465292	0.86[CEU][hapmap]
rs12470702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13428099	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13431014	0.86[CEU][hapmap]
rs16840403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17459758	0.86[CEU][hapmap]
rs17538061	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17538138	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2362787	0.93[EUR][1000 genomes]
rs57709782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60335988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192772	0.91[EUR][1000 genomes]
rs62192773	0.91[EUR][1000 genomes]
rs62192790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192791	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192812	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62192814	0.98[EUR][1000 genomes]
rs62192815	0.98[EUR][1000 genomes]
rs62192816	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62192818	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6435402	0.86[CEU][hapmap]
rs6740362	0.86[CEU][hapmap]
rs72981543	0.95[EUR][1000 genomes]
rs72984907	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72984917	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72984926	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72984930	0.96[EUR][1000 genomes]
rs72984932	0.96[EUR][1000 genomes]
rs7588162	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr2:208912800-208929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:208926000-208927800	Enhancers	K562	blood
3	chr2:208926400-208928800	Enhancers	Fetal Brain Male	brain

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