Variant report

Variant	rs568617
Chromosome Location	chr11:65653242-65653243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr11:65651692-65653280	SK-N-SH	brain:	n/a	chr11:65652282-65652296 chr11:65652301-65652315 chr11:65652282-65652289
2	POLR2A	chr11:65651870-65653606	U87	brain:	n/a	n/a
3	CTCF	chr11:65653200-65653350	GM12875	blood:	n/a	n/a
4	CTCF	chr11:65653100-65653250	AG10803	skin:	n/a	n/a
5	POLR2A	chr11:65651731-65653612	U87	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65650935..65653549-chr11:65685284..65687414,2	MCF-7	breast:
2	chr11:65651325..65654107-chr11:65654178..65656416,6	MCF-7	breast:
3	chr11:65650800..65661192-chr11:65726307..65736419,31	MCF-7	breast:
4	chr11:65652640..65657924-chr11:65769844..65772901,4	MCF-7	breast:
5	chr11:65477746..65479994-chr11:65651413..65653781,3	K562	blood:
6	chr11:65650579..65663306-chr11:65677153..65690311,39	MCF-7	breast:
7	chr11:65429800..65432139-chr11:65653071..65655699,2	MCF-7	breast:
8	chr11:65478750..65480920-chr11:65651843..65654065,2	MCF-7	breast:
9	chr11:65650838..65654244-chr11:65778689..65782514,4	MCF-7	breast:

No data

Variant related genes	Relation type
FIBP	TF binding region
CCDC85B	TF binding region
ENSG00000172977	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000175315	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10791830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1151519	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1204650	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225345	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2231884	1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes]
rs2303385	0.94[ASW][hapmap];0.83[CHB][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs507062	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs583887	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585557	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58568715	0.83[EUR][1000 genomes]
rs588114	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs596002	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs601863	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608616	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs622614	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs625652	0.86[AFR][1000 genomes]
rs641018	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645900	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656980	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs658524	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677931	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs693824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs694994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940691	0.83[CHB][hapmap];0.85[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
10	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
11	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
12	nsv530622	chr11:65649068-65661361	Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs568617	SNX32	cis	Nerve Tibial	GTEx
rs568617	SNX32	cis	Artery Tibial	GTEx
rs568617	FIBP	cis	lymphoblastoid	seeQTL
rs568617	SNX32	cis	Esophagus Mucosa	GTEx
rs568617	RBM14	cis	parietal	SCAN
rs568617	SNX32	cis	Esophagus Muscularis	GTEx
rs568617	SNX32	cis	parietal	SCAN
rs568617	CTSW	cis	Thyroid	GTEx
rs568617	FIBP	cis	multi-tissue	Pritchard
rs568617	SNX32	cis	cerebellum	SCAN
rs568617	SNX32	cis	Artery Aorta	GTEx
rs568617	CTSW	cis	Nerve Tibial	GTEx
rs568617	CTSW	cis	Artery Aorta	GTEx
rs568617	CTSW	cis	Whole Blood	GTEx
rs568617	CTSW	Cis_1M	lymphoblastoid	RTeQTL
rs568617	CTSW	cis	Esophagus Muscularis	GTEx
rs568617	FIBP	Cis_1M	lymphoblastoid	RTeQTL
rs568617	CTSW	cis	Stomach	GTEx
rs568617	CTSW	cis	lymphoblastoid	seeQTL
rs568617	RBM4	cis	cerebellum	SCAN
rs568617	CTSW	cis	Esophagus Mucosa	GTEx
rs568617	FIBP	cis	parietal	SCAN
rs568617	RAB3IL1	cis	cerebellum	SCAN
rs568617	CTSW	cis	Artery Tibial	GTEx
rs568617	CTSW	cis	lung	GTEx
rs568617	SNX32	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65641000-65654400	Weak transcription	Fetal Heart	heart
2	chr11:65641400-65654000	Weak transcription	Small Intestine	intestine
3	chr11:65641600-65655000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:65641600-65655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:65641600-65655000	Weak transcription	Right Atrium	heart
6	chr11:65649000-65653800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:65649000-65654400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:65649000-65654400	Strong transcription	Placenta	Placenta
9	chr11:65649000-65655000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:65649000-65655000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:65649200-65654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:65649200-65654600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:65649400-65654200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:65649400-65654600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:65649600-65654200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:65649600-65654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:65649600-65654600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:65649600-65654600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:65649600-65654600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:65649600-65654800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:65649800-65653400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:65649800-65654400	Strong transcription	Adipose Nuclei	Adipose
23	chr11:65649800-65654400	Strong transcription	Osteobl	bone
24	chr11:65650000-65653400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:65650000-65653800	Strong transcription	NHDF-Ad	bronchial
26	chr11:65650000-65654400	Strong transcription	Fetal Lung	lung
27	chr11:65650000-65654400	Strong transcription	A549	lung
28	chr11:65650000-65654600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr11:65650000-65654600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:65650000-65654600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:65650000-65654800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr11:65650000-65654800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:65650200-65653800	Strong transcription	Primary hematopoietic stem cells	blood
34	chr11:65650200-65654400	Strong transcription	HSMMtube	muscle
35	chr11:65650200-65655000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:65650400-65654200	Strong transcription	HSMM	muscle
37	chr11:65650600-65654400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:65651000-65654400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr11:65651000-65654400	Strong transcription	Left Ventricle	heart
40	chr11:65651200-65654200	Strong transcription	HUVEC	blood vessel
41	chr11:65651600-65654000	Genic enhancers	Fetal Intestine Large	intestine
42	chr11:65651600-65654200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
43	chr11:65651600-65655000	Genic enhancers	Dnd41	blood
44	chr11:65651800-65653400	Genic enhancers	Gastric	stomach
45	chr11:65651800-65654000	Genic enhancers	Fetal Brain Female	brain
46	chr11:65651800-65654000	Genic enhancers	GM12878-XiMat	blood
47	chr11:65651800-65654800	Genic enhancers	NHLF	lung
48	chr11:65651800-65655000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:65651800-65655200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:65652000-65654600	Weak transcription	Liver	Liver

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