Variant report

Variant	rs9455007
Chromosome Location	chr6:70931045-70931046
allele	A/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	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	chr6:70930668-70931076	GM12878	blood:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
5	CTCF	chr6:70930661-70931095	K562	blood:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
6	RAD21	chr6:70930701-70931137	HCT-116	colon:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
7	RAD21	chr6:70930724-70931050	K562	blood:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
8	RAD21	chr6:70930687-70931225	MCF-7	breast:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
9	RAD21	chr6:70930657-70931051	A549	lung:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
10	ZNF143	chr6:70930755-70931058	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr6:70930344-70931590	SK-N-SH	brain:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
12	CTCF	chr6:70930728-70931080	H1-hESC	embryonic stem cell:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
13	RAD21	chr6:70930675-70931080	SK-N-SH_RA	brain:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
14	RAD21	chr6:70930698-70931177	GM12878	blood:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
15	ZMIZ1	chr6:70930896-70931225	K562	blood:	n/a	n/a
16	RAD21	chr6:70930687-70931075	Hela-S3	cervix:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
17	RAD21	chr6:70930674-70931088	H1-hESC	embryonic stem cell:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
18	SMC3	chr6:70930565-70931507	SK-N-SH	brain:	n/a	chr6:70930845-70930859
19	SMC3	chr6:70930701-70931073	GM12878	blood:	n/a	chr6:70930845-70930859
20	CTCF	chr6:70930645-70931106	HepG2	liver:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
21	FOXA1	chr6:70930916-70931371	HepG2	liver:	n/a	n/a
22	CTCF	chr6:70930683-70931057	T-47D	breast:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
23	RAD21	chr6:70930732-70931097	ECC-1	luminal epithelium:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
24	MAX	chr6:70930842-70931271	NB4	blood:	n/a	n/a
25	CTCF	chr6:70930613-70931162	HCT-116	colon:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
26	E2F4	chr6:70930789-70931066	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr6:70931005-70931065	MCF10A-Er-Src	breast:	n/a	n/a
28	CTCF	chr6:70930900-70931050	MCF-7	breast:	n/a	n/a
29	RAD21	chr6:70930276-70931857	SK-N-SH	brain:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
30	RAD21	chr6:70930584-70931169	A549	lung:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
31	RAD21	chr6:70930734-70931094	H1-hESC	embryonic stem cell:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
32	CTCF	chr6:70930753-70931059	K562	blood:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
33	SMC3	chr6:70930724-70931059	HepG2	liver:	n/a	chr6:70930845-70930859
34	RAD21	chr6:70930681-70931076	IMR90	lung:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
35	RAD21	chr6:70930739-70931131	ECC-1	luminal epithelium:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
36	CTCF	chr6:70930678-70931070	IMR90	lung:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
37	CTCF	chr6:70930687-70931122	MCF-7	breast:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
38	CTCF	chr6:70930646-70931094	K562	blood:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
39	RAD21	chr6:70930693-70931280	HepG2	liver:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
40	CTCF	chr6:70930900-70931050	NHLF	lung:	n/a	n/a
41	CTCF	chr6:70930595-70931077	HCT-116	colon:	n/a	chr6:70930845-70930866 chr6:70930848-70930856 chr6:70930843-70930861
42	RAD21	chr6:70930660-70931159	HCT-116	colon:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
43	SMC3	chr6:70930705-70931067	Hela-S3	cervix:	n/a	chr6:70930845-70930859
44	FOXA1	chr6:70931039-70931354	HepG2	liver:	n/a	n/a
45	RAD21	chr6:70930650-70931162	HepG2	liver:	n/a	chr6:70930844-70930863 chr6:70930846-70930853
46	ARID3A	chr6:70930606-70931079	HepG2	liver:	n/a	n/a
47	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: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs73746899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9294863	1.00[ASW][hapmap]
rs9446211	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455002	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455003	0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455004	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9455005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9455007	CST7	trans	lymphoblastoid	seeQTL

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links