Variant report

Variant	rs3945233
Chromosome Location	chr1:86885139-86885140
allele	C/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	chr1:86885076-86885239	GM20000	blood:	n/a	chr1:86885146-86885167
2	RAD21	chr1:86884888-86885406	HCT-116	colon:	n/a	chr1:86885145-86885164
3	CTCF	chr1:86885060-86885210	GM12874	blood:	n/a	chr1:86885146-86885167
4	CTCF	chr1:86885060-86885210	SK-N-SH_RA	brain:	n/a	chr1:86885146-86885167
5	CTCF	chr1:86885051-86885244	Lung_OC	lung:	n/a	chr1:86885146-86885167
6	CTCF	chr1:86885028-86885283	LNCaP	prostate:	n/a	chr1:86885146-86885167
7	CTCF	chr1:86885100-86885250	HEEpiC	esophagus:	n/a	chr1:86885146-86885167
8	CTCF	chr1:86885080-86885230	RPTEC	kidney:	n/a	chr1:86885146-86885167
9	CTCF	chr1:86885009-86885296	GM13977	blood:	n/a	chr1:86885146-86885167
10	CTCF	chr1:86885020-86885170	HL-60	blood:	n/a	chr1:86885146-86885167
11	CTCF	chr1:86885080-86885230	NHDF-neo	bronchial:	n/a	chr1:86885146-86885167
12	CTCF	chr1:86885060-86885210	HA-sp	spinal cord:	n/a	chr1:86885146-86885167
13	CTCF	chr1:86885040-86885190	GM12869	blood:	n/a	chr1:86885146-86885167
14	USF2	chr1:86885033-86885386	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:86885100-86885250	HCM	heart:	n/a	chr1:86885146-86885167
16	CTCF	chr1:86885075-86885233	GM19239	blood:	n/a	chr1:86885146-86885167
17	CTCF	chr1:86885027-86885273	ECC-1	luminal epithelium:	n/a	chr1:86885146-86885167
18	CTCF	chr1:86885080-86885230	WERI-Rb-1	eye:	n/a	chr1:86885146-86885167
19	CTCF	chr1:86884957-86885352	H1-hESC	embryonic stem cell:	n/a	chr1:86885146-86885167
20	CTCF	chr1:86885043-86885295	GM19240	blood:	n/a	chr1:86885146-86885167
21	CTCF	chr1:86885080-86885230	HCM	heart:	n/a	chr1:86885146-86885167
22	CTCF	chr1:86885018-86885370	H1-hESC	embryonic stem cell:	n/a	chr1:86885146-86885167
23	MAZ	chr1:86885000-86885377	K562	blood:	n/a	n/a
24	CTCF	chr1:86885100-86885250	HRPEpiC	eye:	n/a	chr1:86885146-86885167
25	CTCF	chr1:86885080-86885230	SAEC	small airway:	n/a	chr1:86885146-86885167
26	CTCF	chr1:86885080-86885230	GM06990	blood:	n/a	chr1:86885146-86885167
27	CTCF	chr1:86885060-86885210	GM12873	blood:	n/a	chr1:86885146-86885167
28	CTCF	chr1:86885060-86885210	AG04449	skin:	n/a	chr1:86885146-86885167
29	CTCF	chr1:86885040-86885190	A549	lung:	n/a	chr1:86885146-86885167
30	CTCF	chr1:86885080-86885230	GM12871	blood:	n/a	chr1:86885146-86885167
31	SMC3	chr1:86885079-86885275	HepG2	liver:	n/a	n/a
32	RAD21	chr1:86884982-86885214	HepG2	liver:	n/a	chr1:86885145-86885164
33	CTCF	chr1:86885072-86885238	Pancreas_OC	pancreas:	n/a	chr1:86885146-86885167
34	MYC	chr1:86884993-86885194	MCF10A-Er-Src	breast:	n/a	n/a
35	CTCF	chr1:86885041-86885247	HUVEC	blood vessel:	n/a	chr1:86885146-86885167
36	CTCF	chr1:86885060-86885210	GM12867	blood:	n/a	chr1:86885146-86885167
37	CTCF	chr1:86885100-86885250	Hela-S3	cervix:	n/a	chr1:86885146-86885167
38	CTCF	chr1:86885080-86885230	HCT-116	colon:	n/a	chr1:86885146-86885167
39	CTCF	chr1:86885080-86885230	HPF	lung:	n/a	chr1:86885146-86885167
40	CTCF	chr1:86885029-86885263	GM10266	blood:	n/a	chr1:86885146-86885167
41	CTCF	chr1:86885060-86885210	HUVEC	blood vessel:	n/a	chr1:86885146-86885167
42	CTCF	chr1:86885100-86885250	HCT-116	colon:	n/a	chr1:86885146-86885167
43	RAD21	chr1:86884993-86885458	MCF-7	breast:	n/a	chr1:86885145-86885164
44	RAD21	chr1:86885000-86885302	IMR90	lung:	n/a	chr1:86885145-86885164
45	CTCF	chr1:86885080-86885230	AoAF	blood vessel:	n/a	chr1:86885146-86885167
46	CTCF	chr1:86885060-86885210	RPTEC	kidney:	n/a	chr1:86885146-86885167
47	CTCF	chr1:86885100-86885250	BJ	skin:	n/a	chr1:86885146-86885167
48	RAD21	chr1:86885005-86885357	GM12878	blood:	n/a	chr1:86885145-86885164
49	ELF1	chr1:86884969-86885351	K562	blood:	n/a	n/a
50	CTCF	chr1:86885080-86885230	AG10803	skin:	n/a	chr1:86885146-86885167

No.	Distal block	Cell Line	Cell type
1	chr1:86884770..86885617-chr1:86965291..86966347,4	K562	blood:
2	chr1:86885110..86885636-chr1:86939415..86940377,2	K562	blood:
3	chr1:86885099..86885732-chr1:86973485..86974031,3	MCF-7	breast:
4	chr1:86884690..86885606-chr1:86967410..86968457,3	K562	blood:
5	chr1:86884451..86885554-chr1:86967355..86968572,5	MCF-7	breast:
6	chr1:86884686..86885250-chr1:86973632..86974161,2	K562	blood:
7	chr1:86884671..86885639-chr1:86965279..86966251,3	MCF-7	breast:
8	chr1:86884721..86885355-chr1:86966359..86967087,2	K562	blood:
9	chr1:86884967..86885568-chr1:86965463..86966341,2	MCF-7	breast:

Variant related genes	Relation type
CLCA2	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10782571	0.94[ASN][1000 genomes]
rs10873771	0.88[ASN][1000 genomes]
rs10873772	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10873773	0.94[ASN][1000 genomes]
rs10873774	0.92[ASN][1000 genomes]
rs10873775	0.94[ASN][1000 genomes]
rs10873776	0.94[ASN][1000 genomes]
rs10873778	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1116108	0.96[CEU][hapmap]
rs1116109	0.96[ASN][1000 genomes]
rs11161803	0.90[ASN][1000 genomes]
rs11161804	0.90[ASN][1000 genomes]
rs11161805	0.94[ASN][1000 genomes]
rs11161807	0.94[ASN][1000 genomes]
rs11161811	0.98[ASN][1000 genomes]
rs11799437	0.95[CEU][hapmap]
rs11802019	0.92[CEU][hapmap]
rs11810689	0.94[ASN][1000 genomes]
rs12031536	0.90[ASN][1000 genomes]
rs12033867	0.95[ASN][1000 genomes]
rs12072655	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407719	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1407720	0.94[ASN][1000 genomes]
rs1413427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413429	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16908	0.95[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17372196	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1830675	0.88[ASN][1000 genomes]
rs1999600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2031136	0.94[ASN][1000 genomes]
rs2093612	0.92[ASN][1000 genomes]
rs2181418	0.93[ASN][1000 genomes]
rs2210641	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2275000	0.90[ASN][1000 genomes]
rs2275001	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2390057	0.82[CEU][hapmap]
rs2390096	0.94[ASN][1000 genomes]
rs2390097	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2390099	0.94[ASN][1000 genomes]
rs28782251	0.81[AMR][1000 genomes]
rs35173920	0.86[ASN][1000 genomes]
rs3737159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737672	0.96[CEU][hapmap]
rs3765986	0.92[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4534352	0.94[ASN][1000 genomes]
rs4656026	0.90[ASN][1000 genomes]
rs4656044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs58200516	0.94[ASN][1000 genomes]
rs6658025	0.92[ASN][1000 genomes]
rs6674140	0.94[ASN][1000 genomes]
rs6703576	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs67799288	0.94[ASN][1000 genomes]
rs7415758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515651	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7541004	0.86[ASN][1000 genomes]
rs7553685	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs956499	0.96[CEU][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86882200-86885200	Weak transcription	Esophagus	oesophagus
2	chr1:86882200-86894800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:86882400-86885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:86882400-86885200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:86882400-86885200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:86882400-86885200	Weak transcription	Hela-S3	cervix
7	chr1:86884000-86885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:86884200-86885200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:86885000-86885400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:86885000-86885400	Enhancers	Primary hematopoietic stem cells	blood
11	chr1:86885000-86885400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:86885000-86885600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:86885000-86889200	Enhancers	NHEK	skin

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