Variant report

Variant	rs5763779
Chromosome Location	chr22:30504652-30504653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:52)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:52 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr22:30504529-30505031	HCT-116	colon:	n/a	n/a
2	CTCF	chr22:30504288-30505144	SK-N-SH	brain:	n/a	n/a
3	NRF1	chr22:30504443-30505119	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr22:30504615-30504944	HepG2	liver:	n/a	n/a
5	RFX5	chr22:30504236-30505107	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr22:30504629-30505000	K562	blood:	n/a	n/a
7	RAD21	chr22:30504432-30505097	HepG2	liver:	n/a	n/a
8	SMC3	chr22:30504615-30505033	GM12878	blood:	n/a	n/a
9	RAD21	chr22:30504583-30505078	MCF-7	breast:	n/a	n/a
10	ZNF384	chr22:30504575-30505037	GM12878	blood:	n/a	n/a
11	CTCF	chr22:30504596-30505028	IMR90	lung:	n/a	n/a
12	RAD21	chr22:30504443-30505105	A549	lung:	n/a	n/a
13	RAD21	chr22:30504575-30505043	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr22:30504648-30505011	GM12878	blood:	n/a	n/a
15	CTCF	chr22:30504633-30504954	Medullo	brain:	n/a	n/a
16	RAD21	chr22:30504442-30505060	HCT-116	colon:	n/a	n/a
17	CTCF	chr22:30504608-30505012	K562	blood:	n/a	n/a
18	CTCF	chr22:30504636-30504961	GM12878	blood:	n/a	n/a
19	CTCF	chr22:30504610-30504970	MCF-7	breast:	n/a	n/a
20	RAD21	chr22:30504628-30504943	GM12878	blood:	n/a	n/a
21	SMC3	chr22:30504417-30505130	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr22:30504283-30505110	SK-N-SH	brain:	n/a	n/a
23	RAD21	chr22:30504587-30504966	SK-N-SH_RA	brain:	n/a	n/a
24	RAD21	chr22:30504574-30505113	ECC-1	luminal epithelium:	n/a	n/a
25	SMC3	chr22:30504604-30505041	HepG2	liver:	n/a	n/a
26	MAZ	chr22:30504630-30504868	GM12878	blood:	n/a	n/a
27	CTCF	chr22:30504610-30504987	A549	lung:	n/a	n/a
28	SMC3	chr22:30504613-30505050	Hela-S3	cervix:	n/a	n/a
29	SMC3	chr22:30504523-30504999	K562	blood:	n/a	n/a
30	RAD21	chr22:30504565-30505081	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr22:30504648-30505071	SK-N-SH_RA	brain:	n/a	n/a
32	RAD21	chr22:30504567-30505102	IMR90	lung:	n/a	n/a
33	CTCF	chr22:30504642-30504944	A549	lung:	n/a	n/a
34	ARID3A	chr22:30504610-30505004	HepG2	liver:	n/a	n/a
35	RAD21	chr22:30504460-30505108	ECC-1	luminal epithelium:	n/a	n/a
36	RAD21	chr22:30504540-30505027	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr22:30504611-30505023	HepG2	liver:	n/a	n/a
38	RAD21	chr22:30504354-30505149	HCT-116	colon:	n/a	n/a
39	RAD21	chr22:30504624-30505026	GM12878	blood:	n/a	n/a
40	ZNF263	chr22:30504464-30504914	HEK293-T-REx	kidney:	n/a	n/a
41	CTCF	chr22:30504614-30505017	GM12878	blood:	n/a	n/a
42	RAD21	chr22:30504626-30505017	HepG2	liver:	n/a	n/a
43	RAD21	chr22:30504582-30505081	MCF-7	breast:	n/a	n/a
44	CTCF	chr22:30504249-30505138	A549	lung:	n/a	n/a
45	CTCF	chr22:30504562-30505037	MCF-7	breast:	n/a	n/a
46	RAD21	chr22:30504586-30505032	A549	lung:	n/a	n/a
47	CTCF	chr22:30504348-30505093	HCT-116	colon:	n/a	n/a
48	CTCF	chr22:30504634-30504962	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr22:30504625-30505010	Spleen_OC	spleen:	n/a	n/a
50	RAD21	chr22:30504628-30505006	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30504306..30505754-chr22:30651396..30652476,12	MCF-7	breast:
2	chr22:30502959..30506188-chr22:30648757..30654246,8	MCF-7	breast:
3	chr22:30504373..30506765-chr22:30681335..30683680,2	MCF-7	breast:
4	chr22:30504126..30504835-chr22:30682136..30683020,2	K562	blood:
5	chr22:30502809..30506298-chr22:30639806..30643736,4	MCF-7	breast:
6	chr22:30504280..30505360-chr22:30651538..30652426,8	K562	blood:
7	chr22:30504448..30505337-chr22:30651737..30652444,5	MCF-7	breast:
8	chr22:30502612..30504825-chr22:30819472..30821124,2	MCF-7	breast:
9	chr22:30500122..30506829-chr22:30640771..30648697,14	MCF-7	breast:
10	chr22:30503068..30507568-chr22:30652252..30654579,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226573	TF binding region
ENSG00000128342	Chromatin interaction
ENSG00000239282	Chromatin interaction
ENSG00000268812	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1468176	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1548389	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs193471	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs193474	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs193475	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs193476	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1989870	1.00[CEU][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2007446	1.00[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes]
rs2007458	0.92[CEU][hapmap]
rs2285667	0.80[AMR][1000 genomes]
rs2412972	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412976	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41161	0.80[AMR][1000 genomes]
rs41165	0.92[CEU][hapmap]
rs41168	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs41171	1.00[CEU][hapmap]
rs41173	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs41176	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4336042	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4820827	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4823076	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5753008	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5753025	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5753037	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5763670	0.80[AMR][1000 genomes]
rs5763751	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5763775	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5763790	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763842	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7287570	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73164755	0.81[EUR][1000 genomes]
rs737911	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.93[AFR][1000 genomes]
rs9306468	1.00[CEU][hapmap];0.93[AFR][1000 genomes]
rs997913	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5763779	TTC28	cis	cerebellum	SCAN
rs5763779	CABP7	cis	cerebellum	SCAN
rs5763779	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs5763779	MTMR3	cis	parietal	SCAN
rs5763779	ASCC2	cis	cerebellum	SCAN
rs5763779	TTC28AS	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30501400-30505800	Enhancers	A549	lung
2	chr22:30501800-30511800	Weak transcription	Osteobl	bone
3	chr22:30504000-30505600	Enhancers	Dnd41	blood
4	chr22:30504400-30504800	Enhancers	HSMM	muscle
5	chr22:30504400-30504800	Enhancers	NH-A	brain
6	chr22:30504600-30504800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr22:30504600-30504800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr22:30504600-30504800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links