Variant report

Variant	rs939578
Chromosome Location	chr3:112046264-112046265
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:65)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:65 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:112046198-112046571	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr3:112046196-112046677	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr3:112046235-112046562	K562	blood:	n/a	n/a
4	CTCF	chr3:112046240-112046390	A549	lung:	n/a	n/a
5	ATF2	chr3:112046132-112046703	GM12878	blood:	n/a	n/a
6	RAD21	chr3:112046192-112046610	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr3:112046258-112046643	HCT-116	colon:	n/a	n/a
8	RAD21	chr3:112046189-112046704	MCF-7	breast:	n/a	n/a
9	RAD21	chr3:112046140-112046578	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:112046260-112046525	T-47D	breast:	n/a	n/a
11	RUNX3	chr3:112046260-112046701	GM12878	blood:	n/a	n/a
12	CTCF	chr3:112046239-112046552	HUVEC	blood vessel:	n/a	n/a
13	ZNF143	chr3:112046231-112046592	GM12878	blood:	n/a	n/a
14	CTCF	chr3:112046259-112046539	SK-N-SH_RA	brain:	n/a	n/a
15	CTCF	chr3:112046069-112046652	HCT-116	colon:	n/a	n/a
16	RAD21	chr3:112046136-112046683	HCT-116	colon:	n/a	n/a
17	CTCF	chr3:112046259-112046530	Pancreas_OC	pancreas:	n/a	n/a
18	CTCF	chr3:112046203-112046606	A549	lung:	n/a	n/a
19	RAD21	chr3:112046196-112046665	GM12878	blood:	n/a	n/a
20	CTCF	chr3:112046149-112046631	IMR90	lung:	n/a	n/a
21	FOXM1	chr3:112046129-112046657	GM12878	blood:	n/a	n/a
22	CTCF	chr3:112046183-112046615	GM12878	blood:	n/a	n/a
23	SMC3	chr3:112046194-112046813	SK-N-SH	brain:	n/a	n/a
24	STAT3	chr3:112046174-112046374	MCF10A-Er-Src	breast:	n/a	chr3:112046254-112046261
25	CTCF	chr3:112046213-112046581	K562	blood:	n/a	n/a
26	RAD21	chr3:112046185-112046643	IMR90	lung:	n/a	n/a
27	CTCF	chr3:112046260-112046523	HepG2	liver:	n/a	n/a
28	RAD21	chr3:112046195-112046584	GM12878	blood:	n/a	n/a
29	RAD21	chr3:112046235-112046588	HepG2	liver:	n/a	n/a
30	CTCF	chr3:112046190-112046489	A549	lung:	n/a	n/a
31	CTCF	chr3:112046249-112046557	Spleen_OC	spleen:	n/a	n/a
32	CTCF	chr3:112046260-112046410	HFF-Myc	foreskin:	n/a	n/a
33	CTCF	chr3:112046236-112046565	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:112046240-112046390	HCM	heart:	n/a	n/a
35	RAD21	chr3:112045996-112046682	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr3:112046151-112046612	T-47D	breast:	n/a	n/a
37	SMC3	chr3:112046245-112046549	K562	blood:	n/a	n/a
38	CHD1	chr3:112046088-112046630	IMR90	lung:	n/a	n/a
39	TBL1XR1	chr3:112046241-112046346	K562	blood:	n/a	n/a
40	RFX5	chr3:112046242-112046616	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr3:112046245-112046561	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:112046260-112046410	HRPEpiC	eye:	n/a	n/a
43	SMC3	chr3:112046178-112046667	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr3:112046240-112046390	NHLF	lung:	n/a	n/a
45	CTCF	chr3:112046116-112046671	SK-N-SH	brain:	n/a	n/a
46	RAD21	chr3:112046189-112046641	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr3:112046260-112046410	GM12864	blood:	n/a	n/a
48	SMC3	chr3:112046171-112046755	GM12878	blood:	n/a	n/a
49	CTCF	chr3:112046153-112046646	MCF-7	breast:	n/a	n/a
50	CTCF	chr3:112046260-112046410	HEK293	kidney:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:112045925..112046858-chr3:112237972..112238492,2	K562	blood:
2	chr3:112045750..112047025-chr3:112237531..112238950,15	MCF-7	breast:
3	chr3:112045532..112046934-chr3:112156222..112157470,7	MCF-7	breast:
4	chr3:112046007..112046874-chr3:112156015..112156737,3	MCF-7	breast:

No data

Variant related genes	Relation type
CD200	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11714917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716857	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073116	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17513726	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2280462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2399411	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4550804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037521	0.83[ASN][1000 genomes]
rs62264134	0.83[ASN][1000 genomes]
rs62264135	0.83[ASN][1000 genomes]
rs62264136	0.83[ASN][1000 genomes]
rs62264137	0.83[ASN][1000 genomes]
rs6438066	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438067	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6438068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6771014	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774405	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6809034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7619941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs939576	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939577	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814088	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818526	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112041400-112050600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:112041400-112050800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112044800-112050600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:112045200-112046600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:112045400-112046600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:112045600-112046600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:112045600-112046600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:112045800-112046600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr3:112046200-112046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:112046200-112046600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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