Variant report

Variant	rs1200566
Chromosome Location	chr6:70931111-70931112
allele	C/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	CTCF	chr6:70930476-70931335	A549	lung:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
2	NFIC	chr6:70930950-70931434	HepG2	liver:	n/a	n/a
3	RAD21	chr6:70930775-70931152	MCF-7	breast:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
4	CTCF	chr6:70931080-70931230	AG10803	skin:	n/a	n/a
5	RAD21	chr6:70930701-70931137	HCT-116	colon:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
6	CTCF	chr6:70931080-70931230	BJ	skin:	n/a	n/a
7	RAD21	chr6:70930687-70931225	MCF-7	breast:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
8	FOXA2	chr6:70931091-70931356	HepG2	liver:	n/a	n/a
9	CTCF	chr6:70931060-70931210	AG04449	skin:	n/a	n/a
10	CTCF	chr6:70930344-70931590	SK-N-SH	brain:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
11	RAD21	chr6:70930698-70931177	GM12878	blood:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
12	ZMIZ1	chr6:70930896-70931225	K562	blood:	n/a	n/a
13	SMC3	chr6:70930565-70931507	SK-N-SH	brain:	n/a	chr6:70930845-70930859
14	FOXA1	chr6:70930916-70931371	HepG2	liver:	n/a	n/a
15	MAX	chr6:70930842-70931271	NB4	blood:	n/a	n/a
16	CTCF	chr6:70930613-70931162	HCT-116	colon:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
17	FOXA1	chr6:70931109-70931356	HepG2	liver:	n/a	n/a
18	CTCF	chr6:70931060-70931210	NHDF-neo	bronchial:	n/a	n/a
19	RAD21	chr6:70930276-70931857	SK-N-SH	brain:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
20	RAD21	chr6:70930584-70931169	A549	lung:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
21	HNF4A	chr6:70931104-70931359	HepG2	liver:	n/a	chr6:70931260-70931268 chr6:70931260-70931273 chr6:70931261-70931273 chr6:70931259-70931274 chr6:70931259-70931274 chr6:70931261-70931273 chr6:70931260-70931272 chr6:70931259-70931274 chr6:70931259-70931274
22	RAD21	chr6:70930739-70931131	ECC-1	luminal epithelium:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
23	CTCF	chr6:70930687-70931122	MCF-7	breast:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
24	RAD21	chr6:70930693-70931280	HepG2	liver:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
25	RAD21	chr6:70930660-70931159	HCT-116	colon:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
26	FOXA1	chr6:70931039-70931354	HepG2	liver:	n/a	n/a
27	RAD21	chr6:70930650-70931162	HepG2	liver:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
28	MAZ	chr6:70930727-70931208	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:70930597..70933117-chr6:70988758..70990429,2	K562	blood:
2	chr6:70930581..70931580-chr6:71078690..71079470,4	MCF-7	breast:
3	chr6:70930172..70932460-chr6:71107052..71108700,2	K562	blood:
4	chr6:70930395..70931237-chr6:71722269..71722995,2	K562	blood:

Variant related genes	Relation type
ENSG00000253809	TF binding region
ENSG00000112280	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040655	0.85[CEU][hapmap]
rs1200564	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1200565	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1200567	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1517043	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16868641	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16868806	0.87[CEU][hapmap]
rs17690121	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17712342	0.85[EUR][1000 genomes]
rs17747228	0.97[EUR][1000 genomes]
rs45486305	0.97[EUR][1000 genomes]
rs476026	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs476740	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs487928	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs540654	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs558856	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs577010	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs607716	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs661521	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6914511	0.85[CEU][hapmap]
rs6923695	0.85[CEU][hapmap]
rs737331	0.85[EUR][1000 genomes]
rs73746881	0.97[EUR][1000 genomes]
rs9446213	0.85[CEU][hapmap]
rs9455013	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70930000-70932000	Enhancers	Duodenum Mucosa	Duodenum
2	chr6:70930200-70931600	Enhancers	Stomach Mucosa	stomach
3	chr6:70930200-70931800	Enhancers	Fetal Intestine Small	intestine
4	chr6:70930200-70932200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:70930400-70932200	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:70930800-70931400	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:70930800-70931800	Enhancers	Liver	Liver
8	chr6:70931000-70931200	Enhancers	Brain Anterior Caudate	brain
9	chr6:70931000-70931200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr6:70931000-70931400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:70931000-70931400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:70931000-70931400	Enhancers	Adipose Nuclei	Adipose
13	chr6:70931000-70931400	Enhancers	Brain Substantia Nigra	brain
14	chr6:70931000-70931400	Enhancers	Fetal Lung	lung
15	chr6:70931000-70931600	Flanking Active TSS	HepG2	liver

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