Variant report

Variant	rs62305683
Chromosome Location	chr4:88191601-88191602
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:88191460-88191610	HCM	heart:	n/a	n/a
2	RAD21	chr4:88191320-88191706	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr4:88191402-88191656	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr4:88191306-88191725	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr4:88191374-88191602	MCF-7	breast:	n/a	n/a
6	STAT3	chr4:88191429-88191623	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr4:88191175-88191752	HCT-116	colon:	n/a	n/a
8	CTCF	chr4:88191378-88191659	K562	blood:	n/a	n/a
9	SMC3	chr4:88191198-88191815	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr4:88191322-88191658	K562	blood:	n/a	n/a
11	RAD21	chr4:88191374-88191608	K562	blood:	n/a	n/a
12	RAD21	chr4:88191223-88191714	HepG2	liver:	n/a	n/a
13	CTCF	chr4:88191540-88191690	GM12866	blood:	n/a	n/a
14	RAD21	chr4:88191194-88191740	MCF-7	breast:	n/a	n/a
15	RAD21	chr4:88191315-88191699	IMR90	lung:	n/a	n/a
16	ZNF143	chr4:88191337-88191669	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr4:88191353-88191639	GM12878	blood:	n/a	n/a
18	CTCF	chr4:88191349-88191620	K562	blood:	n/a	n/a
19	MAZ	chr4:88191449-88191649	K562	blood:	n/a	n/a
20	RAD21	chr4:88191270-88191720	A549	lung:	n/a	n/a
21	CTCF	chr4:88191311-88191628	MCF-7	breast:	n/a	n/a
22	CTCF	chr4:88191364-88191626	MCF-7	breast:	n/a	n/a
23	ARID3A	chr4:88191313-88191649	HepG2	liver:	n/a	n/a
24	CTCF	chr4:88191378-88191613	Pancreas_OC	pancreas:	n/a	n/a
25	CTCF	chr4:88191382-88191603	NHEK	skin:	n/a	n/a
26	RFX5	chr4:88191402-88191679	Hela-S3	cervix:	n/a	chr4:88191530-88191538
27	CTCF	chr4:88191460-88191610	HAc	cerebellar:	n/a	n/a
28	CTCF	chr4:88191480-88191630	RPTEC	kidney:	n/a	n/a
29	CTCF	chr4:88191219-88191904	A549	lung:	n/a	n/a
30	CTCF	chr4:88191382-88191614	Kidney_OC	kidney:	n/a	n/a
31	CTCF	chr4:88191377-88191646	HepG2	liver:	n/a	n/a
32	RAD21	chr4:88191168-88191866	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr4:88191378-88191612	LNCaP	prostate:	n/a	n/a
34	CTCF	chr4:88191354-88191630	Medullo	brain:	n/a	n/a
35	CTCF	chr4:88191480-88191630	A549	lung:	n/a	n/a
36	CTCF	chr4:88191377-88191608	HUVEC	blood vessel:	n/a	n/a
37	CTCF	chr4:88191350-88191629	Hela-S3	cervix:	n/a	n/a
38	SMC3	chr4:88191299-88192043	Hela-S3	cervix:	n/a	n/a
39	SMC3	chr4:88191337-88191659	K562	blood:	n/a	n/a
40	CTCF	chr4:88191480-88191630	GM12864	blood:	n/a	n/a
41	RAD21	chr4:88191206-88191784	HCT-116	colon:	n/a	n/a
42	MXI1	chr4:88191411-88191632	HepG2	liver:	n/a	n/a
43	ZNF143	chr4:88191401-88191635	K562	blood:	n/a	n/a
44	CTCF	chr4:88191480-88191630	GM12869	blood:	n/a	n/a
45	CTCF	chr4:88191460-88191610	WI-38	lung:	n/a	n/a
46	RAD21	chr4:88191402-88191616	GM12878	blood:	n/a	n/a
47	GATA3	chr4:88191401-88191623	T-47D	breast:	n/a	n/a
48	SMC3	chr4:88191310-88191690	HepG2	liver:	n/a	n/a
49	ZMIZ1	chr4:88191477-88191673	K562	blood:	n/a	n/a
50	RAD21	chr4:88191419-88191625	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88161337..88162947-chr4:88190418..88192890,2	K562	blood:
2	chr4:88132419..88135036-chr4:88191101..88193543,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000250572	TF binding region
ENSG00000145332	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11723697	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726120	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734257	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923434	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55789502	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55947321	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56070439	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083423	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56285151	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305671	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62305677	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305678	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305681	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305682	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305684	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305685	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305686	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305687	0.86[ASN][1000 genomes]
rs62305688	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305693	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305694	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305717	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305718	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305719	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305720	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305721	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62305722	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308868	0.86[ASN][1000 genomes]
rs62308869	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62308871	0.86[ASN][1000 genomes]
rs6531973	0.86[ASN][1000 genomes]
rs6840032	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72670112	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72670120	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72670130	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72670132	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72670133	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7436142	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667669	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668684	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674452	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv516203	chr4:88167878-88228228	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv537171	chr4:88182433-88209309	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv470050	chr4:88186509-88228228	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88190600-88191800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:88191200-88192200	Enhancers	Brain Hippocampus Middle	brain
3	chr4:88191400-88192000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:88191600-88192000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr4:88191600-88192200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:88191600-88192200	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links