Variant report

Variant	rs3904094
Chromosome Location	chr13:37683479-37683480
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	chr13:37683315-37683486	A549	lung:	n/a	chr13:37683404-37683425
2	CTCF	chr13:37683291-37683484	ECC-1	luminal epithelium:	n/a	chr13:37683404-37683425
3	CTCF	chr13:37683360-37683510	GM12878	blood:	n/a	chr13:37683404-37683425
4	CTCF	chr13:37683340-37683490	GM12864	blood:	n/a	chr13:37683404-37683425
5	CTCF	chr13:37683072-37683937	SK-N-SH	brain:	n/a	chr13:37683404-37683425
6	CTCF	chr13:37683380-37683530	HCM	heart:	n/a	chr13:37683404-37683425
7	CTCF	chr13:37683340-37683490	SAEC	small airway:	n/a	chr13:37683404-37683425
8	CTCF	chr13:37683360-37683510	GM12865	blood:	n/a	chr13:37683404-37683425
9	RAD21	chr13:37683177-37683664	A549	lung:	n/a	chr13:37683403-37683422
10	CTCF	chr13:37683360-37683510	HCPEpiC	choroid plexus:	n/a	chr13:37683404-37683425
11	RAD21	chr13:37683135-37683707	ECC-1	luminal epithelium:	n/a	chr13:37683403-37683422
12	CTCF	chr13:37683340-37683490	GM12867	blood:	n/a	chr13:37683404-37683425
13	CTCF	chr13:37683340-37683490	GM12872	blood:	n/a	chr13:37683404-37683425
14	RAD21	chr13:37683275-37683709	MCF-7	breast:	n/a	chr13:37683403-37683422
15	CTCF	chr13:37683340-37683490	RPTEC	kidney:	n/a	chr13:37683404-37683425
16	SMC3	chr13:37683306-37683581	K562	blood:	n/a	chr13:37683404-37683418
17	CTCF	chr13:37683250-37683546	A549	lung:	n/a	chr13:37683404-37683425
18	CTCF	chr13:37683340-37683490	HBMEC	blood vessel:	n/a	chr13:37683404-37683425
19	E2F4	chr13:37683332-37683620	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr13:37683304-37683521	LNCaP	prostate:	n/a	chr13:37683404-37683425
21	CTCF	chr13:37683340-37683490	WERI-Rb-1	eye:	n/a	chr13:37683404-37683425
22	CTCF	chr13:37683360-37683510	GM06990	blood:	n/a	chr13:37683404-37683425
23	CTCF	chr13:37683263-37683552	HUVEC	blood vessel:	n/a	chr13:37683404-37683425
24	CTCF	chr13:37683305-37683527	K562	blood:	n/a	chr13:37683404-37683425
25	CTCF	chr13:37683233-37683503	K562	blood:	n/a	chr13:37683404-37683425
26	CTCF	chr13:37683219-37683641	GM12878	blood:	n/a	chr13:37683404-37683425
27	CTCF	chr13:37683380-37683530	GM12870	blood:	n/a	chr13:37683404-37683425
28	CTCF	chr13:37683340-37683490	GM12874	blood:	n/a	chr13:37683404-37683425
29	CTCF	chr13:37683340-37683490	BJ	skin:	n/a	chr13:37683404-37683425
30	CTCF	chr13:37683360-37683510	NHDF-neo	bronchial:	n/a	chr13:37683404-37683425
31	CTCF	chr13:37683340-37683490	A549	lung:	n/a	chr13:37683404-37683425
32	CTCF	chr13:37683360-37683510	GM12868	blood:	n/a	chr13:37683404-37683425
33	CTCF	chr13:37683360-37683510	GM12874	blood:	n/a	chr13:37683404-37683425
34	CTCF	chr13:37683380-37683530	HCT-116	colon:	n/a	chr13:37683404-37683425
35	CTCF	chr13:37683340-37683490	AG10803	skin:	n/a	chr13:37683404-37683425
36	CTCF	chr13:37683271-37683531	ECC-1	luminal epithelium:	n/a	chr13:37683404-37683425
37	CTCF	chr13:37683293-37683525	Lung_OC	lung:	n/a	chr13:37683404-37683425
38	CTCF	chr13:37683340-37683490	SK-N-SH_RA	brain:	n/a	chr13:37683404-37683425
39	CTCF	chr13:37683360-37683510	Caco-2	colon:	n/a	chr13:37683404-37683425
40	CTCF	chr13:37683380-37683530	GM06990	blood:	n/a	chr13:37683404-37683425
41	SMC3	chr13:37683233-37683577	GM12878	blood:	n/a	chr13:37683404-37683418
42	RAD21	chr13:37683154-37683645	HepG2	liver:	n/a	chr13:37683403-37683422
43	CTCF	chr13:37683302-37683498	Gliobla	brain:	n/a	chr13:37683404-37683425
44	CTCF	chr13:37683282-37683546	Medullo	brain:	n/a	chr13:37683404-37683425
45	CTCF	chr13:37683340-37683490	AoAF	blood vessel:	n/a	chr13:37683404-37683425
46	RAD21	chr13:37683179-37683720	MCF-7	breast:	n/a	chr13:37683403-37683422
47	ARID3A	chr13:37683252-37683528	HepG2	liver:	n/a	n/a
48	CTCF	chr13:37683380-37683530	GM12869	blood:	n/a	chr13:37683404-37683425
49	CTCF	chr13:37683289-37683519	Pancreas_OC	pancreas:	n/a	chr13:37683404-37683425
50	CTCF	chr13:37683340-37683490	GM12871	blood:	n/a	chr13:37683404-37683425

No.	Distal block	Cell Line	Cell type
1	chr13:37683205..37683899-chr13:38176989..38177531,2	K562	blood:
2	chr13:37682944..37683803-chr13:38176643..38177587,6	MCF-7	breast:
3	chr13:37683315..37684009-chr13:38175468..38176096,2	MCF-7	breast:
4	chr13:37683027..37683651-chr8:127339731..127340428,2	MCF-7	breast:

Variant related genes	Relation type
CSNK1A1L	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1009963	0.84[EUR][1000 genomes]
rs11147628	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11147629	0.91[EUR][1000 genomes]
rs11147630	0.91[EUR][1000 genomes]
rs11147632	0.91[EUR][1000 genomes]
rs11620134	0.91[EUR][1000 genomes]
rs1199995	0.86[EUR][1000 genomes]
rs1199996	0.86[EUR][1000 genomes]
rs12583685	0.91[EUR][1000 genomes]
rs12584417	0.91[EUR][1000 genomes]
rs12585998	0.91[EUR][1000 genomes]
rs1336754	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1336762	0.91[EUR][1000 genomes]
rs1764480	0.86[EUR][1000 genomes]
rs1781669	0.86[EUR][1000 genomes]
rs1781670	0.86[EUR][1000 genomes]
rs1856028	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1856029	0.84[EUR][1000 genomes]
rs1937756	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1937757	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1937758	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2997194	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943444	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57671308	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58229785	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6563511	0.90[EUR][1000 genomes]
rs7327617	0.91[EUR][1000 genomes]
rs7334447	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335490	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7981360	0.90[EUR][1000 genomes]
rs7996099	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7996290	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7996605	0.90[EUR][1000 genomes]
rs7996662	0.90[EUR][1000 genomes]
rs8003010	0.86[EUR][1000 genomes]
rs945632	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566176	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9566181	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566183	0.90[EUR][1000 genomes]
rs9566184	0.90[EUR][1000 genomes]
rs9566185	0.90[EUR][1000 genomes]
rs9566186	0.90[EUR][1000 genomes]
rs9566187	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576171	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576172	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576173	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576184	0.91[EUR][1000 genomes]
rs9576185	0.89[EUR][1000 genomes]
rs9576186	0.90[EUR][1000 genomes]
rs9576187	0.90[EUR][1000 genomes]
rs9576188	0.90[EUR][1000 genomes]
rs9576189	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576190	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576192	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37681600-37685000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr13:37682200-37684200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
3	chr13:37682800-37683800	Enhancers	Osteobl	bone
4	chr13:37682800-37684000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:37682800-37684000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr13:37683000-37684600	Enhancers	Fetal Lung	lung
7	chr13:37683200-37684200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:37683400-37684000	Enhancers	Colon Smooth Muscle	Colon
9	chr13:37683400-37684200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr13:37683400-37684200	Enhancers	Fetal Stomach	stomach

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