Variant report

Variant	rs17123615
Chromosome Location	chr1:62900128-62900129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:62899980-62900130	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr1:62900000-62900150	HMF	breast:	n/a	n/a
3	CTCF	chr1:62900020-62900170	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:62900020-62900170	HRE	kidney:	n/a	n/a
5	CTCF	chr1:62899980-62900130	AG09319	gingival:	n/a	n/a
6	CTCF	chr1:62900040-62900190	HMF	breast:	n/a	n/a
7	SMC3	chr1:62899947-62900271	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr1:62900020-62900170	HEK293	kidney:	n/a	n/a
9	CTCF	chr1:62900040-62900190	HPAF	blood vessel:	n/a	n/a
10	CTCF	chr1:62900020-62900170	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:62899604-62903300	HepG2	liver:	n/a	n/a
12	CTCF	chr1:62900040-62900190	HBMEC	blood vessel:	n/a	n/a
13	CTCF	chr1:62900113-62900154	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:62899934-62903502	SK-N-MC	brain:	n/a	n/a
15	CTCF	chr1:62900020-62900170	AG09309	skin:	n/a	n/a
16	CTCF	chr1:62900020-62900170	RPTEC	kidney:	n/a	n/a
17	CTCF	chr1:62900080-62900165	GM12878	blood:	n/a	n/a
18	CTCF	chr1:62900104-62900131	GM10248	blood:	n/a	n/a
19	CTCF	chr1:62900004-62900206	IMR90	lung:	n/a	n/a
20	CTCF	chr1:62899980-62900130	HCM	heart:	n/a	n/a
21	CTCF	chr1:62900060-62900210	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr1:62900000-62900150	HPAF	blood vessel:	n/a	n/a
23	CTCF	chr1:62900032-62900193	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:62899936-62903273	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:62899313-62903762	GM12891	blood:	n/a	n/a
26	CTCF	chr1:62900023-62900219	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:62899650-62900330	MCF10A-Er-Src	breast:	n/a	n/a
28	ARID3A	chr1:62900027-62900175	HepG2	liver:	n/a	n/a
29	CTCF	chr1:62900060-62900210	AG04450	lung:	n/a	n/a
30	POLR2A	chr1:62899384-62900168	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr1:62900060-62900210	HBMEC	blood vessel:	n/a	n/a
32	CTCF	chr1:62900040-62900190	BE2_C	brain:	n/a	n/a
33	RAD21	chr1:62899917-62900282	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr1:62900080-62900230	HEEpiC	esophagus:	n/a	n/a
35	SMC3	chr1:62899953-62900241	HepG2	liver:	n/a	n/a
36	RAD21	chr1:62899869-62900289	HepG2	liver:	n/a	n/a
37	RAD21	chr1:62899929-62900257	HepG2	liver:	n/a	n/a
38	CTCF	chr1:62900000-62900150	NHEK	skin:	n/a	n/a
39	CTCF	chr1:62900080-62900230	GM12864	blood:	n/a	n/a
40	CTCF	chr1:62900080-62900230	GM12873	blood:	n/a	n/a
41	CTCF	chr1:62900060-62900210	WERI-Rb-1	eye:	n/a	n/a
42	CTCF	chr1:62900020-62900170	Caco-2	colon:	n/a	n/a
43	CTCF	chr1:62900040-62900190	AG04449	skin:	n/a	n/a
44	CTCF	chr1:62900020-62900170	HCPEpiC	choroid plexus:	n/a	n/a
45	CTCF	chr1:62899949-62900291	GM12878	blood:	n/a	n/a
46	CTCF	chr1:62900060-62900210	AG09309	skin:	n/a	n/a
47	CTCF	chr1:62900000-62900150	MCF-7	breast:	n/a	n/a
48	CTCF	chr1:62900029-62900170	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr1:62899980-62900130	GM12878	blood:	n/a	n/a
50	CTCF	chr1:62900047-62900170	Medullo	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62899539..62901299-chr1:62907455..62909142,2	MCF-7	breast:
2	chr1:62862539..62865270-chr1:62897710..62900697,2	K562	blood:

No data

Variant related genes	Relation type
USP1	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493323	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10493325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs1168050	1.00[CHB][hapmap]
rs1168121	1.00[EUR][1000 genomes]
rs12023489	1.00[JPT][hapmap]
rs12062275	1.00[CHB][hapmap]
rs12563308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[EUR][1000 genomes]
rs12563863	1.00[EUR][1000 genomes]
rs12565895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[EUR][1000 genomes]
rs12566265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1408480	1.00[EUR][1000 genomes]
rs17123688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17123694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17123705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17123712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17123721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[EUR][1000 genomes]
rs17123725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[EUR][1000 genomes]
rs17123740	1.00[EUR][1000 genomes]
rs17123743	1.00[EUR][1000 genomes]
rs2016736	1.00[EUR][1000 genomes]
rs34898550	1.00[EUR][1000 genomes]
rs36157139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3737890	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55709519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56094630	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56193814	1.00[EUR][1000 genomes]
rs56792530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57022388	1.00[EUR][1000 genomes]
rs59505425	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59662235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59816054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60339595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs610248	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61308091	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61501887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74076653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74076654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74076668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076670	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74076907	1.00[EUR][1000 genomes]
rs74076909	1.00[EUR][1000 genomes]
rs74078610	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74078643	1.00[EUR][1000 genomes]
rs74078661	1.00[EUR][1000 genomes]
rs9436224	1.00[JPT][hapmap]

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	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62890600-62901000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:62891000-62901000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:62891000-62901000	Weak transcription	NHEK	skin
4	chr1:62892200-62900800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:62895000-62901000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:62895200-62900200	Weak transcription	HepG2	liver
7	chr1:62895600-62900800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:62895600-62900800	Weak transcription	HMEC	breast
9	chr1:62895600-62901000	Weak transcription	HSMMtube	muscle
10	chr1:62899200-62900200	Enhancers	Fetal Heart	heart
11	chr1:62899800-62900200	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:62899800-62901000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:62899800-62901000	Weak transcription	NHDF-Ad	bronchial
14	chr1:62900000-62900200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:62900000-62900400	Enhancers	Brain Hippocampus Middle	brain
16	chr1:62900000-62901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:62900000-62901000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:62900000-62901000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:62900000-62901000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:62900000-62901000	Weak transcription	HSMM	muscle

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