Variant report

Variant	rs4812690
Chromosome Location	chr20:41816349-41816350
allele	A/C
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	RAD21	chr20:41816281-41816793	H1-hESC	embryonic stem cell:	n/a	chr20:41816557-41816576
2	RAD21	chr20:41816301-41816752	ECC-1	luminal epithelium:	n/a	chr20:41816557-41816576
3	CTCF	chr20:41816320-41816470	A549	lung:	n/a	n/a
4	CEBPB	chr20:41816312-41816697	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr20:41816330-41816935	PFSK-1	brain:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
6	CTCF	chr20:41816318-41816896	MCF-7	breast:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
7	RAD21	chr20:41816257-41816831	MCF-7	breast:	n/a	chr20:41816557-41816576
8	REST	chr20:41816265-41816903	ECC-1	luminal epithelium:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
9	RAD21	chr20:41816307-41816746	SK-N-SH_RA	brain:	n/a	chr20:41816557-41816576
10	CUX1	chr20:41816328-41816615	K562	blood:	n/a	n/a
11	CTCF	chr20:41816330-41816697	A549	lung:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
12	SIN3AK20	chr20:41816281-41816903	MCF-7	breast:	n/a	n/a
13	CTCF	chr20:41816288-41816751	T-47D	breast:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
14	REST	chr20:41816311-41816792	HepG2	liver:	n/a	chr20:41816422-41816430
15	REST	chr20:41816269-41816892	PANC-1	pancreas:	n/a	chr20:41816422-41816430
16	RAD21	chr20:41816302-41816755	Hela-S3	cervix:	n/a	chr20:41816557-41816576
17	REST	chr20:41816279-41816886	A549	lung:	n/a	chr20:41816422-41816430
18	RAD21	chr20:41816339-41816739	SK-N-SH_RA	brain:	n/a	chr20:41816557-41816576
19	CTCF	chr20:41816020-41817330	SK-N-SH	brain:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
20	REST	chr20:41816336-41816862	PFSK-1	brain:	n/a	chr20:41816422-41816430
21	RAD21	chr20:41816140-41816828	H1-hESC	embryonic stem cell:	n/a	chr20:41816557-41816576
22	REST	chr20:41816127-41817149	HL-60	blood:	n/a	chr20:41816422-41816430 chr20:41816893-41816902 chr20:41817115-41817122
23	REST	chr20:41816233-41816964	MCF-7	breast:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
24	RAD21	chr20:41816198-41816865	HCT-116	colon:	n/a	chr20:41816557-41816576
25	RAD21	chr20:41816319-41816827	HCT-116	colon:	n/a	chr20:41816557-41816576
26	REST	chr20:41816122-41817095	H1-neurons	neurons:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
27	CTCF	chr20:41816342-41816792	K562	blood:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
28	RAD21	chr20:41816235-41816817	A549	lung:	n/a	chr20:41816557-41816576
29	REST	chr20:41816279-41816958	ECC-1	luminal epithelium:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
30	CTCF	chr20:41815955-41816953	A549	lung:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
31	TEAD4	chr20:41816304-41816835	A549	lung:	n/a	n/a
32	RAD21	chr20:41816342-41816776	GM12878	blood:	n/a	chr20:41816557-41816576
33	SMC3	chr20:41816244-41816833	HepG2	liver:	n/a	chr20:41816561-41816571 chr20:41816561-41816575
34	CTCF	chr20:41816280-41816787	HCT-116	colon:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
35	RAD21	chr20:41816209-41817252	H1-hESC	embryonic stem cell:	n/a	chr20:41816557-41816576
36	RAD21	chr20:41816311-41816853	ECC-1	luminal epithelium:	n/a	chr20:41816557-41816576
37	RAD21	chr20:41816336-41816783	HepG2	liver:	n/a	chr20:41816557-41816576
38	RAD21	chr20:41816310-41816874	MCF-7	breast:	n/a	chr20:41816557-41816576
39	RAD21	chr20:41815974-41817339	SK-N-SH	brain:	n/a	chr20:41816557-41816576 chr20:41817274-41817287
40	REST	chr20:41816207-41816985	PANC-1	pancreas:	n/a	chr20:41816422-41816430 chr20:41816893-41816902
41	RAD21	chr20:41816223-41816830	HepG2	liver:	n/a	chr20:41816557-41816576
42	POU2F2	chr20:41816347-41816777	GM12878	blood:	n/a	chr20:41816531-41816546 chr20:41816532-41816544 chr20:41816534-41816543 chr20:41816533-41816543 chr20:41816535-41816542 chr20:41816530-41816548 chr20:41816533-41816543
43	SMC3	chr20:41816128-41817262	SK-N-SH	brain:	n/a	chr20:41816561-41816571 chr20:41816561-41816575
44	CTCF	chr20:41816319-41816779	HepG2	liver:	n/a	chr20:41816561-41816574 chr20:41816560-41816576 chr20:41816559-41816577 chr20:41816561-41816574
45	REST	chr20:41816339-41816807	H1-hESC	embryonic stem cell:	n/a	chr20:41816422-41816430
46	RAD21	chr20:41816316-41816869	A549	lung:	n/a	chr20:41816557-41816576
47	SMC3	chr20:41816282-41816784	GM12878	blood:	n/a	chr20:41816561-41816571 chr20:41816561-41816575
48	SMC3	chr20:41816281-41816783	Hela-S3	cervix:	n/a	chr20:41816561-41816571 chr20:41816561-41816575

No.	Distal block	Cell Line	Cell type
1	chr20:40832583..40833565-chr20:41816153..41816980,6	MCF-7	breast:
2	chr20:40584685..40585561-chr20:41816130..41816774,5	MCF-7	breast:
3	chr20:40832079..40832639-chr20:41816078..41817042,2	K562	blood:
4	chr20:41816163..41817038-chr20:42037697..42038566,2	K562	blood:

Variant related genes	Relation type
ENSG00000233508	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2867655	0.82[ASN][1000 genomes]
rs4812689	0.92[AFR][1000 genomes]
rs6016973	0.82[ASN][1000 genomes]
rs6065588	0.81[ASN][1000 genomes]
rs926288	0.84[AFR][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	nsv1063450	chr20:41409901-41880620	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1060690	chr20:41413369-41851935	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1066088	chr20:41417205-42060036	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2751914	chr20:41744586-41890453	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41815400-41819000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr20:41816000-41816400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
3	chr20:41816000-41816600	Enhancers	Brain Hippocampus Middle	brain
4	chr20:41816200-41816400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
5	chr20:41816200-41816400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr20:41816200-41816400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr20:41816200-41816400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:41816200-41816400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr20:41816200-41816400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:41816200-41816400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
11	chr20:41816200-41816600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr20:41816200-41816600	Enhancers	Brain Angular Gyrus	brain
13	chr20:41816200-41816600	Active TSS	Brain Anterior Caudate	brain
14	chr20:41816200-41816800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:41816200-41816800	Bivalent Enhancer	Fetal Brain Male	brain
16	chr20:41816200-41816800	Bivalent Enhancer	Fetal Stomach	stomach

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