Variant report

Variant	rs11053821
Chromosome Location	chr12:10653897-10653898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:10653504-10654184	HCT-116	colon:	n/a	n/a
2	CTCF	chr12:10653760-10653910	NB4	blood:	n/a	n/a
3	CTCF	chr12:10653695-10653910	A549	lung:	n/a	n/a
4	NRF1	chr12:10653848-10653901	GM12878	blood:	n/a	n/a
5	CTCF	chr12:10653453-10654221	A549	lung:	n/a	n/a
6	CTCF	chr12:10653780-10653930	HPF	lung:	n/a	n/a
7	CTCF	chr12:10653580-10654066	MCF-7	breast:	n/a	n/a
8	CTCF	chr12:10653780-10653930	GM12865	blood:	n/a	n/a
9	CTCF	chr12:10653780-10653930	GM12874	blood:	n/a	n/a
10	CTCF	chr12:10653780-10653930	GM12878	blood:	n/a	n/a
11	RAD21	chr12:10653658-10653914	SK-N-SH_RA	brain:	n/a	n/a
12	RAD21	chr12:10653630-10654016	HepG2	liver:	n/a	n/a
13	CTCF	chr12:10653840-10653990	HRE	kidney:	n/a	n/a
14	CTCF	chr12:10653820-10653970	A549	lung:	n/a	n/a
15	SMC3	chr12:10653624-10653999	GM12878	blood:	n/a	n/a
16	CTCF	chr12:10653677-10653954	K562	blood:	n/a	n/a
17	SMC3	chr12:10653504-10654073	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr12:10653607-10654117	HCT-116	colon:	n/a	n/a
19	CTCF	chr12:10653729-10653920	Pancreas_OC	pancreas:	n/a	n/a
20	RFX5	chr12:10653516-10654122	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:10653584-10654062	A549	lung:	n/a	n/a
22	SMC3	chr12:10653700-10653930	K562	blood:	n/a	n/a
23	CTCF	chr12:10653780-10653930	GM12867	blood:	n/a	n/a
24	RAD21	chr12:10653589-10653972	GM12878	blood:	n/a	n/a
25	SMC3	chr12:10653647-10653995	HepG2	liver:	n/a	n/a
26	CTCF	chr12:10653644-10653972	K562	blood:	n/a	n/a
27	CTCF	chr12:10653780-10653930	HepG2	liver:	n/a	n/a
28	CTCF	chr12:10653642-10653966	IMR90	lung:	n/a	n/a
29	CTCF	chr12:10653731-10653926	K562	blood:	n/a	n/a
30	RAD21	chr12:10653523-10654117	A549	lung:	n/a	n/a
31	E2F4	chr12:10653390-10653951	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr12:10653760-10653910	HPAF	blood vessel:	n/a	n/a
33	CTCF	chr12:10653840-10653990	HVMF	connective:	n/a	n/a
34	CTCF	chr12:10653760-10653910	HPF	lung:	n/a	n/a
35	CTCF	chr12:10653760-10653910	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr12:10653634-10653989	GM12878	blood:	n/a	n/a
37	CTCF	chr12:10653760-10653910	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr12:10653707-10653947	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr12:10653760-10653910	WERI-Rb-1	eye:	n/a	n/a
40	RAD21	chr12:10653515-10654116	A549	lung:	n/a	n/a
41	CTCF	chr12:10653820-10653970	HMEC	breast:	n/a	n/a
42	CTCF	chr12:10653744-10653913	LNCaP	prostate:	n/a	n/a
43	RAD21	chr12:10653643-10653967	A549	lung:	n/a	n/a
44	RAD21	chr12:10653692-10653961	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr12:10653653-10654073	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr12:10653760-10653910	AG04449	skin:	n/a	n/a
47	RAD21	chr12:10653381-10654044	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:10653760-10653910	HMEC	breast:	n/a	n/a
49	CTCF	chr12:10653780-10653930	HCFaa	heart:	n/a	n/a
50	CTCF	chr12:10653860-10654010	HAc	cerebellar:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:10388252..10388816-chr12:10653557..10654233,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180574	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10845152	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10845155	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs11053820	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053827	1.00[CEU][hapmap]
rs11053839	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11053849	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12299741	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12300017	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs7296695	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7966228	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9668890	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8914	chr12:10532300-10662676	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv557456	chr12:10532326-10698255	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases
3	nsv898764	chr12:10537269-10698255	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv898765	chr12:10537269-10701992	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv898766	chr12:10537269-10722585	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv557457	chr12:10545925-10698255	Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv557458	chr12:10546140-10698255	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv557459	chr12:10560591-10729821	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv557477	chr12:10601690-10698255	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv557478	chr12:10604945-10698255	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv898772	chr12:10622047-10722585	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv557479	chr12:10644663-10729821	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1042090	chr12:10646985-10695398	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv973197	chr12:10650348-10662298	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11053821	RPL13AP20	cis	cerebellum	SCAN
rs11053821	PTMS	cis	cerebellum	SCAN
rs11053821	CLEC4E	cis	parietal	SCAN
rs11053821	CLEC1A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10652400-10656800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr12:10652800-10654200	Enhancers	Hela-S3	cervix
3	chr12:10653800-10654200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:10653800-10654200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links